I got the intake swapped and the motor back together and running good. I took the time to do a full cooling system flush with distilled water and refilled the cooling system with G-05 coolant and distilled water since 99 was the only year Ford tried to use Dex-Cool. See why I did this
HERE.
Swapping the intake is fairly straightforward. The only PITA part of the job is getting the big bracket (the shop manual calls this the "crash bracket." I think it should be called the "cash bracket" since it is the one thing that would make most home mechanics take this job to a shop or dealer) on the back of the driver's side cylinder head off. The top bolt comes out easy enough, but there is a bolt on the back of the driver's side cylinder head that is a pisser to get to.
To get this bracket off, you first remove the throttle body. Removal of the throttle body is easily accomplished, even without any directions, but there are directions available in many places on the internet as well as in the factory service manual.
You then must remove the wire loom support bracket that is bolted on over the crash bracket. The following picture is what the crash bracket and loom brackets would look like if you were viewing the back of the cylinder head with the brackets bolted in place:
The smaller thinner bracket is held on by a bolt and a nut. The nut screws down onto the stud that protrudes from the bolt that holds the crash bracket on. In other words, to get the crash bracket bolt off, you need to remove the loom bracket too.
This is what you would see on the back of the cylinder head if the loom bracket were removed:
The bolt and nut for the loom bracket are 13 MM. The bolt for the crash bracket is a 15 MM. It is a super tight fit to get your hand and a wrench down the back of the motor since where you are working is directly below the wiper motor which is covered by the cowl. If you can pull the cowl, more power to you, but I don't think it would give you much extra room since the wiper motor is right there anyway. Also, I tried to remove the cowl but couldn't get the wiper arms off the studs they are pressed onto.
The one real "trick" to getting these bolts off is to get 13 MM and 15 MM ratcheting box end wrenches. There isn't really room for a socket unless you have TINY hands. You could do this job with a standard box end wrench, but it would take you forever. I bought a set of metric ratcheting box ends and they did the trick.
When I put the motor back together, I left off the loom bracket since it did nothing but support the wiring harness. The harness is wrapped in electrical tape and is inside a plastic loom, so it isn't going to sag anyway. I also didn't put the rear bolt in the crash bracket. I was going to leave the crash bracket off entirely since it also serves no real function, but I ended up having to re-use it since the top bolt is also an intake manifold bolt and I couldn't source a bolt the right size to replace it on Sunday. The crash bracket is back in place but is only held on by the top bolt.
Hopefully these pictures and my tips will help others who do this swap in the future. I can't figure out why Ford put those brackets on the motor. They really serve no purpose. I don't know why it is called a crash bracket either. The only thing it would protect in a crash would be the valve cover, and if you were in a crash so serious that this bracket would offer any protection, the car (and probably you) would be a total loss anyway.
The only other suggestion I have is to tie the wrench you are working with to your wrist. If you drop a wrench back behind the motor, you are screwed unless it falls all the way down to the ground. While I was doing this I dropped three wrenches back there and was unable to retrieve them until the intake had been removed. Fortunately, I have somehow managed to collect lots of spare metric box end wrenches over the years. If you only have one wrench set, tie the wrench to your wrist or risk getting stymied mid project.
