"I am wondering if there possibly is an air bubble in the system, as I was only able to add one gallon of antifreeze."
Yes, leave the cap loose (or out), massage the hoses to assist the air out while the car is idling.
"I have not installed the filler panel at the bottom of the front bumper, and I got to thinking, before the accident my SE never had that black plastic filler piece. I got one with the SVT front clip, good or bad if not on?"
You need to reinstall the lower radiator air deflector. This forces air to the radiator to help cool it.
"I searched the board, and saw postings for the water pump issue, mine is a late 1998 SE, and I was wondering now if I should have inspected the water pump while the car was apart. Too late now, of course! it's all back together.
I swore I thought I heard a sqeaking by the water pump, but I am not sure now it wasn't just the idler puller for the belt."
Remove the 3 bolts from the top black plastic cover. Tensioner has marks on it to show if it is past its useful life. New Dayco belt is $12.
"Does anyone have a suggestion for a dealer service book?"
Haynes is pretty good too but the Ford Factory CD is the best. I will PM you. And Autozone has some good info too.
http://www.autozone.com/servlet/UiBroker?UseCase=RG001&UserAction=beginRepairGuide.
"I fixed the a/c and now it's blowing colder than before. Nice surprise. Only issue is I notice while under the car, alot of red dust on the compressor, and lower engine.
At around 89k, would it be time to do the compressor clutch?
not making noise, just trying to be preventative."
Wipe the dust off with a wet cloth. Then don't worry about it until it breaks down.
Good luck.
