2003 LS V6 engine dies after ~90 seconds

LeedsAL

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I need a Lincoln LS V6 expert. My car is a 2003 Lincoln LS with 3.0L V6 engine and automatic transmission, manufactured January 2003, 150K miles (VIN 1LNHM86S93Y659890). This is the 2nd-generation car with throttle-by-wire and PCV valve on driver's side valve cover. I love it but I'm beginning to love to hate it.

Sorry for the long post but I'm trying to include enough detail to give a good picture of the problem.

I bought this used car a few months ago and have enjoyed it. "Auto-Check" indicated good history and previous owner indicated he had purchased the car used in 2006 and had maintained it well. Until a few weeks ago, it ran great. A few weeks ago, it went into "limp-home" mode without prior warning or other symptoms. When the tow-truck arrived to haul it to my home, I was surprised to find it started normally and could be driven onto the truck bed. I had it towed anyway out of concern it might fail again (instrument panel showed both the "wrench" symbol and the check-engine light). After I got it home, I drove it and found that it would run 5-6 minutes, then cut off as though there was no ignition; 2-3 minutes later, it would start again and run 5-6 more minutes.

I drove it to Autozone and asked them to read codes in the diagnostic system. They found the following.
P0446
P0606
P1235
P2107
P2110

Because I've researched this forum enough to know these cars are sensitive to coils and plugs, I replaced all 6 of both (Motorcraft OEM plugs, gapped correctly, and Hungarian-made Visteon coils). Thanks to the articles I found here, I was able to do the work myself. All the old plugs were OEM Motorcraft and looked like they were burning correctly. Of the six old coils, only four were OEM Motorcraft so I assume at least two had been replaced previously. No oil in spark plug wells or other evidence of leaks at valve-cover gaskets, intake manifold air valves, or PCV sysytem. I pulled the upper intake manifold but not the lower manifold. I re-used the six upper intake manifold gaskets after careful cleaning and inspection (no gasket sealant, just re-installed them "naked") and torqued everything properly.

When I put everything back together and tried to start the car to bleed the cooling system, I found the battery almost dead as though something had been draining it. I have no idea what might have caused that ... hadn't noticed anything before and hadn't experienced any prior problems. It's a new Interstate Megatron, purchased by previous owner. Although the battery barely had enough power to crank the car, it did eventually start. Since then, the car seems to have similar problem as before only now it won't run 5-6 mintues ... runs only 60-90 seconds, then dies (but can be re-started immediately). It won't run long enough to allow the cooling system to be bled.

I've seen forum posts suggesting the problem could be leaking intake gaskets, throttle body, or faulty engine management computer. To rule out the easiest of the 3, I replaced the upper intake gaskets I'd re-used initially with new ones from local Lincoln dealer. While I had the intake manifold removed, I also checked the ignition transformers to make sure they're grounded properly to the rear side the motor. Also checked to make sure there's continuity of throttle body wires from throttle body to PCM.

I need advice regarding how to further test throttle body and computer, also any other ideas you might have about what the problem might be. Check-engine light and wrench light is still on. Since I haven't been able to drive back to Autozone to get codes read again, I finally bought a scanner. The battery was completely disconnected for hours yesterday while I was working on the car so I assume any stored codes were erased. After I put the intake manifold back on last night, I re-connected the battery and started the car. As usual, it ran for apprx 90 seconds and died (check-engine light and wrench light on, no response to accelerator pedal). I connected the scanner and found apprx 20 codes (!) ... most of them related to transmission and throttle body. I can't imagine what's causing transmission codes ... the car hasn't been shifted out of Park for since I parked it in the driveway after my initial visit to Autozone to have the codes read days ago.

Thanks in advance for your help. I'm running out of patience with this car.
 
It looks like a bad PCM. What were the twenty codes?

Please note that the battery you have is not the correct (safe) battery for this car. You need one with a single vent tube connection.
 
Interesting. I've had the same problem in the past where a vehicle will die and do nothing to the point that you want to call a tow truck just to have it start normally several hours later. Turned out to be a fuel pump issue. It's also possible that you killed the battery trying to start it when it crapped out. If the battery was marginal to begin with, this would kill it quickly. Some of the original codes were related to fuel system issues as well. Based on this, I would suggest that you replace the fuel pump and the battery.

Since you already know the battery is defective though, start with it before anything else. With a known good battery, you can retry running the car with all codes clear, and get a fresh read on it. A bad battery can cause all kinds of voltage ghosts (patent pending) to appear on a computerized car. A fresh start with a new battery will eliminate all these transient problems and whatever codes set again should be real. Unless the battery is just old, I'd also look at having the alternator checked out as a battery and an alternator are symbiotic, and when one dies it usually takes the other with it. What happens is the alternator will blow its diodes out trying to charge a bad battery, or a battery will kill itself trying to run the car with no charge input. I see you say it's a new battery, but even new batteries can be defective.

If you continue to have the problems after the battery replacement, then I'd look at doing the fuel pump, fuel pump sock (if the LS uses them) and the fuel filter. Then go from there.

One kinda odd thing is the car running for 90 seconds then dying. That sounds like a possible venting issue, which you also set a code for. If the tank isn't venting, then the fuel pump may be depressurizing the tank to the point that it can no longer push fuel out of it. When the car dies, the fuel comes back in, and the defective vent allows enough air to pass in before a restart is attempted to let the car run again.

Hope some of this helps. Unfortunately, with the myriad codes you have set you're going to have to just fix one thing, then see where it sits before moving to the next step, and I would start with the battery since it's now a known bad.
 
Battery is new within last 12 months … Interstate Megatron Plus MTP-66 … has single oval-shaped side vent on negative-terminal side which appears to exactly fit the car’s OEM vent hose … battery otherwise sealed (no way to check the water). Looks like it was designed for this application. I removed it from the car and took it to Autozone tonight for testing; they report it 100% good.
I’m unfamiliar with the new scanner ($100 bucks from Wally World) but last night after the car ran for 2 min it read 12 “generic” codes and 1 Ford-specific code as follows: P2104 P0606 P0708 P0743 P0755 P0765 P1235(Ford) P2107 P2198 P0138 P0750 P2196.
After the generic codes, the scanner asked for car manufacturer and ran a “KOEO Ford/Mazda enhanced test” scan to come up with the following 20 Ford/Mazda codes. P0060 P0121 P0480 P0708 P0713 P0740 P0743 P0748 P0750 P0753 P0755 P0758 P0765 P0768 P0960 P1000 P1702 P2104 P2121 P2122.
Thanks for your help.
 
Okay, sorry - you do have an acceptable battery. I should have looked it up first.
So, either you have a lot of wiring chewed through or knocked off, or a bad PCM. P0606 says the PCM is bad.
 
Joegr ... thanks. No wiring problems that I've been able to find. Do you think PCM is more likely than throttle body?

If PCM, do you have any tips about where to get one and how to get it "flash-programmed" to match the car. I've seen some used/reman ones on ebay and I figure they're probably a lot less expensive than new from Lincoln. What's your opinion on them? Also, would you trust the P0606 code indicating the PCM is bad or would you take it to Lincoln to have it tested by them?

If throttle body, do you have any tips on aftermarket availability or would you go strictly OEM new from Lincoln?
 
On the battery, did they deep load test or just do a quick check? A deep load test takes about 15-20 minutes to complete and is the only really valid test to prove the battery is really good. A battery with a damaged cell will pass the quick test but will fail the deep load. If it checked out on the longer test, it'll need to spend some time on the charger.

On the PCM, the Lincoln dealer should be able to flash the program into another PCM for you for an hour's shop time. You'll need to call them to ask what they require to do this. They will at the very least need your VIN and the new PCM, and they may need the PCM in the car requiring a tow truck ride. Or, as an alternative you can see if this Torrie fellow everyone keeps talking up can do it. Since he does programming, he likely can dump a stock program in for you. No idea on cost.

If the battery is indeed good, then a bad PCM will also cause a ton of unrelated codes to come up. And as every time you pull codes you seem to get more of them...
 
... They will at the very least need your VIN and the new PCM, and they may need the PCM in the car requiring a tow truck ride. ...

They need to have the whole car, with the replacement PCM in it. They have to put the PCM and the cluster (PATS) into secure mode and then marry them together.
 
150k+ miles, not sure of its history, and 20+ codes... let your local lincoln dealer diagnose it in my opinion. they will at least put you on the right path for about $100. I think all anyone can do is shoot from the hip without looking at the car. get lincoln/ford dealer's report and then pick and choose what you want to repair, what you want them to repair, and what you dont want to repair at all. i would probably come back to the forum with the diagnosis report with any questions
 
Based on forum feedback, my hunch is that the ECM is bad. I’m guessing the initial problem was coils and plugs but that I damaged the ECM when I re-started the car with weak battery; that’s when things really seemed to begin journey from bad to worse.

I pulled the ECM and sent to a company in Texas to be remanufactured (goecm.com); for apprx $300, they promise quick turnaround, lifetime warranty, and no need for dealer re-flash. After I get it re-installed, I’ll post follow-up.

Thanks to everyone for all the help. I love this car but have the feeling it’s going to require more ongoing TLC than I’m willing to invest. :)
 
hmm $300 is an expensive guess in my book.. good luck tho
 
The car is finally fixed. Thanks to all who took the time to read my post and give me input. Here’s the update.

GOECM told me the processor in my ECM was bad and it therefore couldn’t be rebuilt. They said a bad processor is the only part in the LS’ ECM that precludes them attempting to rebuild it … anything else can be fixed. Despite the fact they were unable to repair my ECM, their customer service is good and I would recommend them without hesitation for any ECM problem (goecm.com).

Anyway, I found a used ECM on ebay for $250. I installed it and had the car towed to local Lincoln dealer to be reflashed. Since then, everything seems to be fine. The car runs better than before (new coils and plugs :D) and I’m falling in love with it again.

One note regarding ECM replacement. On my car, the 3 plugs that attach the wiring harness to the ECM need to be bolted in rather than just plugged in. If only pushed into place instead of having the bolts tightened, the plugs don’t seem to fit deeply enough in the ECM sockets to make good electrical contact. This is a pain if you’re disconnecting plugs at the ECM to check wiring continuity to various components because you can’t just push the plugs back into the ECM socket; you must take a little extra time to screw the plug bolts in.
 

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