Just bought a 2004 Lincoln Ls, need help

Yash

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Hey guys I bought a 2004 Lincoln LS V6 with 90,000 miles recently. I traded my 2000 Toyota Celica and $1,600 for it. I thought it was a pretty good deal. My Celica had 142,000 miles, the exterior and interior was in really rough shape, and it had multiple cylinders with misfires. I valued the Celica at about $1,000 so in my eyes I paid $2,600 for the LS. Before I explain, I want to say that I have done a lot of research on google, youtube, and this forum prior to posting this thread.

At first glance the car seemed really nice but I quickly noticed it had a bunch of problems. There was a major roof leak that caused water damage to the interior of the car. I fixed the roof leak pretty quickly with silicone. For the most part there aren't any major stains in the interior. There is really bad water damage (stain) on the driverside speaker, door, and steering wheel which I'm hoping I can very carefully paint over. The storage part of the trunk (under the base where the donut lies) is all rusted from water damage, so I also plan on painting that over.

But the water damage is the least of my worries. The service engine light popped up after a few days of driving. I got a P0430 code which is "Catalyst system efficiency below threshold bank 2". I did some research and put some CAT Cleaner in the tank. Nothing happened. Next I decided to change the oxygen sensors. The car itself drives very smooth and the engine doesn't make any noise so I assumed that the catalytic converter was in good shape. After I changed the sensors, I reset the service engine light and unfortunately, it popped back up. Now I'm thinking the catalytic converter is going bad. Anyone have any advice? I would hate to replace the catalytic converter because I feel like its going to cost $500-$1000. Luckily, I don't have to do it IMMEDIATELY because the inspection is good till February.

Another big problem is the A/C. The A/C does not work at all and blows BURNING hot air. I took it to my mechanic and he replaced a blown fuse and purged/recharged the system with refrigerant but it still did not work. He said that when he tried to turn the A/C on the compressor was not kicking on and he thinks it might be an electrical problem. He told me to bring it to a Lincoln dealer. I did the diagnostic test and got the codes 27 98 and 12 65 pop up. I did some research and found a lot of posts about the DCCV valve. I Read these two threads which were helpful:

Hot air comes from A/C, how to locate the the faulty parts?

DCCV Fuse. Check it!

From what I read the 12 65 is a dummy code that doesn't have anything to do with this model. The 27 98 is the DCCV circuit short to ground which means the valve could be bad or the wiring could be bad. I am tempted to buy the valve and replace, but I'd hate to spend the money and it not solve the problem. Is there anything I can do before replacing the valve? I am not opposed to buying a volt meter and checking resistance, voltage, and continuity. I just need to get walked through it because I have no background in electrical stuff. Also, my ABS and traction control randomly turns on while I'm driving which makes me think there is an electrical problem.
 
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I got a P0430 code which is "Catalyst system efficiency below threshold bank 2".

Another user reported this same code. Here is the link: Code p0430?Code p0430?

J
oegr's reply nails it. Sum it up: It could be O2 sensor or the O2 monitor are failing. Possibly your cats are likely clogged. Why are they clogged? "Most likely you have some marginal COPs (coils) and that is letting some raw gasoline make it down to the cats".
In other words, start with replacing all your spark plugs and the COPs at the same time. Use Motorcraft COPs if affordable, otherwise seek a brand name, stay away from cheap ebay COPs.
Worst case scenario, locate Magnaflow cats, will cost significantly less than Fomoco and magnaflow makes a solid exhaust for the LS.


Another big problem is the A/C. The A/C does not work at all and blows BURNING hot air. I took it to my mechanic and he replaced a blown fuse and purged/recharged the system with refrigerant.
Blown fuse on the DCCV does indicate the control module has failed.
Double check correct refrigerant is used. I found mulitple sources say thew LS uses UAC RO0900B PAG 46 (R-134a) Oil. Lincoln Refrigerant and oil capacity charts || TechChoice Parts
Please correct me if this is wrong ^

I think the correct way to diagnose the AC issue is to check and see if compressor is getting power. I'm not too knowledgeable here so I wont be too much help, but since you already replaced fuses and the gas, and checked for leaks, and can confirm no compressor action, then this would be my next step. If compressor has power, then next I would tackle what is the compressor actuator (which I think is DCCV, guys please correct me if im wrong).
 
...Blown fuse on the DCCV does indicate the control module has failed.
Double check correct refrigerant is used. I found mulitple sources say thew LS uses UAC RO0900B PAG 46 (R-134a) Oil. Lincoln Refrigerant and oil capacity charts || TechChoice Parts
Please correct me if this is wrong ^

I think the correct way to diagnose the AC issue is to check and see if compressor is getting power. I'm not too knowledgeable here so I wont be too much help, but since you already replaced fuses and the gas, and checked for leaks, and can confirm no compressor action, then this would be my next step. If compressor has power, then next I would tackle what is the compressor actuator (which I think is DCCV, guys please correct me if im wrong).

Sorry, but that is pretty much all wrong.

The blown fuse points to the DCCV.
The DCCV (Dual Coolant Control Valve) has nothing to do with the compressor or it's electric clutch, other than they are both powered by the same fuse.
There's too much trouble shooting to cover it all in one post. Lets take this one problem at a time and see where we get.

Experience says that's it 99% likely to be your DCCV that is shorted, but there are some tests you can do first.
2006 Lincoln LS Workshop Manual
scroll down to H10 and start there.

When you replace the valve, use the Motorcraft one. The aftermarket ones often don't work well and only last a few months.
 
Oh, and you are going to need this too: 2006 Lincoln LS Workshop Manual -- brought to you by Owlman
Unfortunately, it doesn't cover the V6, but everything else should be correct for you.

Do you have a moon roof, or was the leak at the windshield?

I have a moon roof but that wasn't the problem. The leak was coming from the windshield and door.

Sorry, but that is pretty much all wrong.

The blown fuse points to the DCCV.
The DCCV (Dual Coolant Control Valve) has nothing to do with the compressor or it's electric clutch, other than they are both powered by the same fuse.
There's too much trouble shooting to cover it all in one post. Lets take this one problem at a time and see where we get.

Experience says that's it 99% likely to be your DCCV that is shorted, but there are some tests you can do first.
2006 Lincoln LS Workshop Manual
scroll down to H10 and start there.

When you replace the valve, use the Motorcraft one. The aftermarket ones often don't work well and only last a few months.

Okay so this is a little overwhelming but here's where I am with my thought process.

As far as the catalytic converter goes I replaced all the oxygen sensors with these: https://www.amazon.com/gp/product/B01MYX3HY3/ref=ppx_yo_dt_b_asin_title_o05_s00?ie=UTF8&psc=1

I bought them because they were cheap and I am really trying to avoid putting money into this car. I bought a Foseal OBD2 Scanner and now two new codes are popping up!! I am getting P0133 and P0153 in addition to the P0430. So now there's something wrong with the upstream sensors on both bank 1 and 2. I had a feeling that the downstream sensors were designed differently than the upstream sensors. The sensors that I ordered are all the same so maybe that is the problem? Only thing is according to the workshop manual (V8): 2006 Lincoln LS Workshop Manual -- brought to you by Owlman2006 Lincoln LS Workshop Manual -- brought to you by Owlman the upstream and downstream sensors have the same part number. Any input would be helpful. I'm going to jack the car up and look at the upstream sensors. Right now my two options are to check for a leak and tighten the sensors or reinstall the old sensors.

Now I really like this car but I'm starting to wonder if putting all this money into it is worth it. Right now I'm stuck between spending all this money on replcing the spark plugs, coils, and catalytic converter or just selling it and getting my money back. I have to fix the A/C because I feel like no one is going to buy it without A/C. If I do sell it I want $3,000 for it at the least. But like I said I really like this car and I'm not opposed to spending money on it, I am just worried that it will keep having problems later on.

Found 6 sets of coils and plugs for $50: Set of 6 Bosch Spark Plugs + 6 ADP Ignition Coils For Lincoln LS & Jaguar S-Type | eBay

I talked to the dealer and they gave me an estimate for replacing the catalytic converter. He said it will cost around $700 to replace bank 2. I was thinking that if I get one replaced, I might as well get the other one replaced too right? Now I know you guys always reccomend quality parts like the magnaflows but I can't justify paying $400+ for a cat when there are cheaper options. The one that the dealer is going to use is $300: Advance Auto Parts - Down for Maintenance

I found the same one on Ebay for $200: Catalytic Converter-Ultra Direct Fit Converter fits 03-04 Lincoln LS 3.0L-V6 | eBay

There's also an Evan Fischer one for $150: New Catalytic Converter for 2003-2005 Lincoln LS Right (Passenger) Side 723650419731 | eBay

So best case scenario, assuming the labor costs $200, I spend $350 - $400 on getting the catalytic converter replaced with a cheap part. Lets say I want to keep the car for a long time then I'll buy the magnaflows which are $400 a pop, plus $300 for labor, I'm looking at $1100 total. In that case if I care about the car I'll have to replace the oxygen sensors with quality ones. That will put the total money I spent on the car at $4500. And that doesn't include what I'm gonna have to spend on the A/C. Kinda hurts because at that point im putting more money into it then the car will ever be worth.

As far as the A/C goes I still have to buy a voltmeter and trouble shoot the circuit. I was able to get the bolt off the DCCV without disconnecting the antifreeze hose above it which will save me a lot of work. My question is if I decide to replace the DCCV with a new one (I will have to disconnect the three tubes which might cause coolant to leak out) will I have to purge the system and recharge it? And it still might not fix the problem. Also, if I have to bleed it out and refill it, how do I do that? What kind of coolant does it take? I just realized I disconnected the DCCV the other day when I was messing around with it to see how hard it would be to replace. I have been driving with it disconnected. Is that dangerous? Does the DCCV control the cooling system for the engine too? I haven't noticed any overheating of the engine.

Thanks for all your help guys. I'll post pictures and updates soon.
 
I have a moon roof but that wasn't the problem. The leak was coming from the windshield and door.



Okay so this is a little overwhelming but here's where I am with my thought process.

As far as the catalytic converter goes I replaced all the oxygen sensors with these: https://www.amazon.com/gp/product/B01MYX3HY3/ref=ppx_yo_dt_b_asin_title_o05_s00?ie=UTF8&psc=1

I bought them because they were cheap and I am really trying to avoid putting money into this car. I bought a Foseal OBD2 Scanner and now two new codes are popping up!! I am getting P0133 and P0153 in addition to the P0430. So now there's something wrong with the upstream sensors on both bank 1 and 2. I had a feeling that the downstream sensors were designed differently than the upstream sensors. The sensors that I ordered are all the same so maybe that is the problem? Only thing is according to the workshop manual (V8): 2006 Lincoln LS Workshop Manual -- brought to you by Owlman2006 Lincoln LS Workshop Manual -- brought to you by Owlman the upstream and downstream sensors have the same part number. Any input would be helpful. I'm going to jack the car up and look at the upstream sensors. Right now my two options are to check for a leak and tighten the sensors or reinstall the old sensors.

Now I really like this car but I'm starting to wonder if putting all this money into it is worth it. Right now I'm stuck between spending all this money on replcing the spark plugs, coils, and catalytic converter or just selling it and getting my money back. I have to fix the A/C because I feel like no one is going to buy it without A/C. If I do sell it I want $3,000 for it at the least. But like I said I really like this car and I'm not opposed to spending money on it, I am just worried that it will keep having problems later on.

Found 6 sets of coils and plugs for $50: Set of 6 Bosch Spark Plugs + 6 ADP Ignition Coils For Lincoln LS & Jaguar S-Type | eBay

I talked to the dealer and they gave me an estimate for replacing the catalytic converter. He said it will cost around $700 to replace bank 2. I was thinking that if I get one replaced, I might as well get the other one replaced too right? Now I know you guys always reccomend quality parts like the magnaflows but I can't justify paying $400+ for a cat when there are cheaper options. The one that the dealer is going to use is $300: Advance Auto Parts - Down for Maintenance

I found the same one on Ebay for $200: Catalytic Converter-Ultra Direct Fit Converter fits 03-04 Lincoln LS 3.0L-V6 | eBay

There's also an Evan Fischer one for $150: New Catalytic Converter for 2003-2005 Lincoln LS Right (Passenger) Side 723650419731 | eBay

So best case scenario, assuming the labor costs $200, I spend $350 - $400 on getting the catalytic converter replaced with a cheap part. Lets say I want to keep the car for a long time then I'll buy the magnaflows which are $400 a pop, plus $300 for labor, I'm looking at $1100 total. In that case if I care about the car I'll have to replace the oxygen sensors with quality ones. That will put the total money I spent on the car at $4500. And that doesn't include what I'm gonna have to spend on the A/C. Kinda hurts because at that point im putting more money into it then the car will ever be worth.

As far as the A/C goes I still have to buy a voltmeter and trouble shoot the circuit. I was able to get the bolt off the DCCV without disconnecting the antifreeze hose above it which will save me a lot of work. My question is if I decide to replace the DCCV with a new one (I will have to disconnect the three tubes which might cause coolant to leak out) will I have to purge the system and recharge it? And it still might not fix the problem. Also, if I have to bleed it out and refill it, how do I do that? What kind of coolant does it take? I just realized I disconnected the DCCV the other day when I was messing around with it to see how hard it would be to replace. I have been driving with it disconnected. Is that dangerous? Does the DCCV control the cooling system for the engine too? I haven't noticed any overheating of the engine.

Thanks for all your help guys. I'll post pictures and updates soon.

How and Who confirmed you need new Cats? Before you decide to flip it or keep it you need to make sure 100% that it needs new Cats or just good trustworthy NGK O2 Sensors

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More Information for NTK 22060


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NGK Spark plugs gapped to proper specs
    • Apply a light film of silicone brake caliper grease and dielectric compound to the inside of the coil boots before installation.

  • s6x~us~en~file=a0068503.gif~gen~ref.gif
MotorCraft COP's (Coil Over Plugs) Yes they are expensive but these will be a one and done fix
Last but not least a good synthetic Oil and Shell V-Power® NiTRO+ Premium Gasoline
The only reason I'm adding my 2 cents is the simple fact I was getting a CEL for the * P0455 Evaporative Emission Control System Leak Detected (gross leak) ...happen to be a faulty fuel cap but it was also triggering P0430 after fixing the p0455 code the p0430 code went away also...ppl jump to conclusions so fast when it could be many things that trigger p0430...it could be leaking intake manifold or leaking coolant ...make sure you diagnose the car correctly before you spend hundreds on CATS!
Good Luck!
 
...As far as the catalytic converter goes I replaced all the oxygen sensors with these: https://www.amazon.com/gp/product/B01MYX3HY3/ref=ppx_yo_dt_b_asin_title_o05_s00?ie=UTF8&psc=1...

Cheap O2 sensors are a really bad idea for any car, let alone the LS.

...I bought them because they were cheap and I am really trying to avoid putting money into this car. ...

Boy, did you buy the wrong car!

...I am getting P0133 and P0153 in addition to the P0430. So now there's something wrong with the upstream sensors on both bank 1 and 2. I had a feeling that the downstream sensors were designed differently than the upstream sensors. The sensors that I ordered are all the same so maybe that is the problem? Only thing is according to the workshop manual (V8): 2006 Lincoln LS Workshop Manual -- brought to you by Owlman2006 Lincoln LS Workshop Manual -- brought to you by Owlman the upstream and downstream sensors have the same part number. ...

Yep, you need the correct O2 sensors. No, they are not the same part number. The service manual only gives the base part of the part numbers. You need the full part numbers.


Please read some of the threads on here. Cheap coils are very often a disaster, and can damage your PCM. Don't do it. Just dump the car now. Don't torture it.
Also, my experience is that Bosch plugs and Ford don't go together well.

... I was able to get the bolt off the DCCV without disconnecting the antifreeze hose above it which will save me a lot of work. My question is if I decide to replace the DCCV with a new one (I will have to disconnect the three tubes which might cause coolant to leak out) will I have to purge the system and recharge it? And it still might not fix the problem. Also, if I have to bleed it out and refill it, how do I do that? What kind of coolant does it take? I just realized I disconnected the DCCV the other day when I was messing around with it to see how hard it would be to replace. I have been driving with it disconnected. Is that dangerous? Does the DCCV control the cooling system for the engine too? I haven't noticed any overheating of the engine.

Thanks for all your help guys. I'll post pictures and updates soon.

Just take the top radiator hose off. That makes it way easier.
Yes, you will have to drain and refill the cooling system. There is a very specific fill and bleed procedure to follow.
You can use the universal long life pre-mixed Prestone.
The DCCV does not control engine cooling.
 
Considering you actually have a code for catalyst issues, I would concentrate on that.

Cop's are a big issue on this vehicle, but throwing hundreds of dollars of parts at a car without proper diagnostics or any diagnostics for that matter is a waste of money.

If raw fuel can damage a catalytic converter, than how can a bad o2 sensor causing a rich condition not do the same?

Forget the cop's and fix what the car is telling you is bad and go from there.

People on this forum throw cop's at every problem. Bad cat? Cop's. Misfire? cop's. Bad fuel mileage, must need cop's. Used Chinese cop's? That's obviously why your transmission isn't shifting correctly, replace cop's. Before you know it you threw $600 in cop's and plugs at a bad cat or o2 sensor issue that could have cost you $25 or less to fix.

I went through the same thing. Everything everyone said came down to Cop's.

I ended up with a bad injector and needing a solenoid pack for my transmission. I also replaced the valve body while I was in there and added a shift kit. I dropped a $1000 between cop's , plugs, injectors , valve body and solenoid pack and the fluids to accompany that job. Car shifts and runs great now. But if your going to own this vehicle be prepared to drop money even if you do the work.

Follow your codes. Forget the AC for the time being and concentrate on getting your car running right. Work on the cat's/o2 sensor issues for now.

If possible purchase a ford compatible OBD2 USB from eBay , with the switch and download forscan to a laptop. The OBD2 is 10-15 I believe.

This will open up a whole new level of diagnostics for you.

Good luck
 
If raw fuel can damage a catalytic converter, than how can a bad o2 sensor causing a rich condition not do the same?

Running rich won't kill cats nearly as fast as dumping raw fuel. Running rich is still pretty limited. Bad o2s eventually get flagged and the PCM reverts to it's own

Considering you actually have a code for catalyst issues, I would concentrate on that.

...

Forget the cop's and fix what the car is telling you is bad and go from there.

It would suck to replace a cat and have the new one go bad in a month because the cause of the failed cat was never fixed

People on this forum throw cop's at every problem. Bad cat? Cop's. Misfire? cop's. Bad fuel mileage, must need cop's. Used Chinese cop's? That's obviously why your transmission isn't shifting correctly, replace cop's. Before you know it you threw $600 in cop's and plugs at a bad cat or o2 sensor issue that could have cost you $25 or less to fix.

I went through the same thing. Everything everyone said came down to Cop's.

I ended up with a bad injector and needing a solenoid pack for my transmission.

The symptoms of a solenoid pack and COP-induced transmission problems are generally different. Solenoid pack failure often shows early signs at the 2-3 shift. Bucking at around 50mph at light throttle up a slight hill is very much a COP issue. Injectors do occasionally fail and throw similar misfire symptoms and codes. If COPs don't fix it, they're a possible next step.

But yes, if you don't know the age or quality of the current COPs, it really is as common of an issue as we make it out to be. OP already threw the chap parts at it - o2 sensors

If possible purchase a ford compatible OBD2 USB from eBay , with the switch and download forscan to a laptop. The OBD2 is 10-15 I believe.

This will open up a whole new level of diagnostics for you.

Good luck

That, I agree with
 
I'm not coming on here to debate , but when the first thing mentioned to replace is cop's for a bad cat with no misfire code and zero vehicle history, no complaint of misfire. Then I would say the COP paranoia is real.

I am not dismissing the possibility, nor am I dismissing the fact it's a real issue on this engine, but throwing $500 of oem coils at a bad cat makes zero sense in an troubleshooting mentality.

And dumping raw fuel is running rich, this can be achieved by bad injectors and or spark related issues. Maybe we should replace all cop's and go from there?

Also, cats clog. Sometimes for a current reason, sometimes for past reason and sometimes for an unknown reason. I personally feel cutting the cats off for a peek would prove most efficient if o2 sensors prove okay. Here's a link to the many causes of a clogged catalytic converter. Reasons For A Converter Failure

Op, follow the codes. Check out o2 sensors, check cats next. Then chase the squirrels.
 
Another user reported this same code. Here is the link: Code p0430?Code p0430?

J
oegr's reply nails it. Sum it up: It could be O2 sensor or the O2 monitor are failing. Possibly your cats are likely clogged. Why are they clogged? "Most likely you have some marginal COPs (coils) and that is letting some raw gasoline make it down to the cats".
In other words, start with replacing all your spark plugs and the COPs at the same time. Use Motorcraft COPs if affordable, otherwise seek a brand name, stay away from cheap ebay COPs.
Worst case scenario, locate Magnaflow cats, will cost significantly less than Fomoco and magnaflow makes a solid exhaust for the LS.

I am assuming 'COP' is the ignition coil? What does COP stand for exactly? Can someone explain to me how an improperly sealed ignition coil can cause gasoline to leak into the cats? From my understanding the coils are in the top of the engine. I just don't understand how there is something wrong with my cats when the engine runs soo smoothly. If my cats were clogged there should be loss of power, vibration, or some type of mechanical symptom.

How and Who confirmed you need new Cats? Before you decide to flip it or keep it you need to make sure 100% that it needs new Cats or just good trustworthy NGK O2 Sensors

You make a good point here. If my cats are bad then replacing them wouldn't solve the problem because the new ones would eventually be destroyed as well if I don't fix what is causing the deterioration. So first I need to figure out what the real problem is.

Considering you actually have a code for catalyst issues, I would concentrate on that.

Follow your codes. Forget the AC for the time being and concentrate on getting your car running right. Work on the cat's/o2 sensor issues for now.

If possible purchase a ford compatible OBD2 USB from eBay , with the switch and download forscan to a laptop. The OBD2 is 10-15 I believe.

This will open up a whole new level of diagnostics for you.

Good luck

This is good advice, thank you.

Also, cats clog. Sometimes for a current reason, sometimes for past reason and sometimes for an unknown reason. I personally feel cutting the cats off for a peek would prove most efficient if o2 sensors prove okay. Here's a link to the many causes of a clogged catalytic converter. Reasons For A Converter Failure

This link is very helpful.

Possible causes:

1. Excess fuel entering exhaust - could be caused by an incorrect fuel mixture, incorrect timing, corroded spark plugs, a faulty oxygen sensor. I am 99% sure my cylinders are not misfiring because there is no code for it and the engine runs very smoothly. It is possible that there is an incorrect fuel mixture caused by faulty oxygen sensors. I recently installed the old upstream oxygen sensors back onto my cats because of the P133 and P153 codes I got after I put the new ones on. I reset the codes and I am waiting to see what happens.

2. Oil or Antifreeze Entering Exhaust - The symptoms of this would be loss of power and/or overheated engine parts. Once again my engine runs smooth and my temperature gauge on the dashboard is not signalling any excess heat.

3. Deteriorated Spark Plug or Spark Plug Wires - This would cause excess engine fuel to leak into cats. Excess engine fuel in the cats would combust, overheat the cat, and destroy the substrate/filament inside. This is a possibility, however it seems that if this was occurring it would escalate quickly.

4. Oxygen Sensor Not Functioning Properly - This could cause the engine to run too rich or too lean. Too rich means there is excess gas which I covered above. I read somewhere else that if an engine runs too rich the exhaust will have a rotten egg smell which my car does not. Too lean means there is too much air. I read this can be caused by a dirty fuel filter, O2 sensor, air mass flow sensor, or an air leak.

Also I read the car can be a little jerky if the engine is running lean. I have noticed that the transmission doesn't shift very smoothly. Its hard to describe but there are subtle and not so subtle clunks and jerks when it shifts between gears.

I'd also like to note that my fuel economy is pretty good. I get 23 miles per gallon on my commute to work everyday (lots of traffic lights and stopping/going). And on the weekends if I do long drives I get as much as 30 miles per gallon.

5. Road Damage or Broken Hangers

Just take the top radiator hose off. That makes it way easier.
Yes, you will have to drain and refill the cooling system. There is a very specific fill and bleed procedure to follow.
You can use the universal long life pre-mixed Prestone.
The DCCV does not control engine cooling.

Do you think I could get away with using hose clamps? I feel like if I clamp off the hoses I shouldn't lose any coolant or have any air bubbles manifest in the lines. Also I noticed my cooling fan and compressor does not kick on when I turn on the A/C. Does this information signal any possible causes?
 
I am assuming 'COP' is the ignition coil? What does COP stand for exactly? ...

Coil On Plug

... Can someone explain to me how an improperly sealed ignition coil can cause gasoline to leak into the cats? ...

If water (usually rain water) gets into the plug well, it will short the secondary of the coil such that little or no power makes it to the spark plug. No spark = no combustion = raw fuel out the exhaust. If it hits most of the time and misses some of the time, the PCM will not set a code for misfire and will not turn the fuel off to that cylinder. This is why marginal failures are so bad. Complete failure of a coil would set a code and would cause the fuel injector to be turned off for that cylinder.

Prolonged exposure to water can cause internal corrosion of the coil and failure even when dry later. Prolonged exposure to oil will degrade the coil boot insulation and can cause shorts to the sides of the plug wells. (Note that oil exposure is not as bad as it was initially thought to be, but can still be a problem.)

With an enhanced Ford scan tool, you can read the pre-misfire counts for each cylinder. This is where I find marginal coils. It almost never sets an actual misfire code.

... I just don't understand how there is something wrong with my cats when the engine runs soo smoothly. If my cats were clogged there should be loss of power, vibration, or some type of mechanical symptom...

You are correct. Of course we are assuming that you know how much power is supposed to be there. Has you driven other gen II LSes?

...Also I read the car can be a little jerky if the engine is running lean. I have noticed that the transmission doesn't shift very smoothly. Its hard to describe but there are subtle and not so subtle clunks and jerks when it shifts between gears...

Sadly, this could be the normal operation of the transmission. Have you tried other LSes? Neither of mine are as smooth shifting as other cars I have or have had. This is true from day one and mile ten or so. My 04 is still the same (pretty good) at 240K or so miles. I had to get the one on my 06 rebuilt a little before 200K miles. It is a little rougher than the 04 now, but he did rebuild it to be stronger than new, so I think this is a consequence of that.
 
With an enhanced Ford scan tool, you can read the pre-misfire counts for each cylinder. This is where I find marginal coils. It almost never sets an actual misfire code.
Joe, where can one get an enhanced Ford scan tool without spending a fortune? Do you have any in mind, would be interested in getting one.
 
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Coil On Plug

If water (usually rain water) gets into the plug well, it will short the secondary of the coil such that little or no power makes it to the spark plug. No spark = no combustion = raw fuel out the exhaust. If it hits most of the time and misses some of the time, the PCM will not set a code for misfire and will not turn the fuel off to that cylinder. This is why marginal failures are so bad. Complete failure of a coil would set a code and would cause the fuel injector to be turned off for that cylinder.

Prolonged exposure to water can cause internal corrosion of the coil and failure even when dry later. Prolonged exposure to oil will degrade the coil boot insulation and can cause shorts to the sides of the plug wells. (Note that oil exposure is not as bad as it was initially thought to be, but can still be a problem.)

Okay that is very helpful. So I should be able to take out the coils and plugs inspect them for water damage/corrosion?

You are correct. Of course we are assuming that you know how much power is supposed to be there. Has you driven other gen II LSes?

I have never driven an LS before this one. I did notice, however when I first bought the car the engine was idling at 1500 RPM. After I changed the oxygen sensors the engine idles at 750 RPM now.

I am going to look into that Ford diagnostic tool.
 
After skimming all of this and reading water damage, cats, electrical issues and such... I'm gonna go way out in left field and say this vehicle was partially submerged in water for a time.
 
After skimming all of this and reading water damage, cats, electrical issues and such... I'm gonna go way out in left field and say this vehicle was partially submerged in water for a time.

Theres a leak in my roof, I haven’t been able to fix it completely. Although it is odd the storage part of the trunk is rusted to hell
 
So here's an update:

I reinstalled the old upstream sensors that were originally on my cats and all the codes went away. I kept the cheap sensors I got from amazon on the downstream connections. I reset the codes and they didn't come back for 100s of miles. BUT the engine started idling very low (750 RPM) which I knew was not good. When I first bought it the car idled at 1500 RPM.

You guys were totally right about using cheap oxygen sensors. It's causing more problems for my car now. When I start it up it has no power and doesn't want to drive. RPMs are super low and it wants to bog out. I have to put it into 1st or 2nd gear to get it driving properly. I am getting a P0301 Cylinder 1 misfire detected and P0316 Engine misfire detected on startup (first 1000 revolutions) in addition to the P0430 Catalyst system efficiency below threshold.

Can you guys recommend the right/quality oxygen sensors for this car? Downstream and Upstream. I should've done it right the first time.
 
... BUT the engine started idling very low (750 RPM) which I knew was not good. When I first bought it the car idled at 1500 RPM...

750 is correct for a warm engine. Even a cold one requires less than a minute before it drops to 750. 1500 indicates a big problem.
 
I also would suspect that the previous owner had coil problems... and drove it that way for a while... which caused the dumping of raw gas into the CATS... and is why you are getting catalyst efficiency codes for the converter. The previous owner probably unloaded the car when he/she got sticker shock from new cat prices.

Aside from this... I will add that cheap parts and shortcuts never work out well for the LS... or the owner.
 

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