If the neons were yellow, you'd be at +100 crank hp.

Answers to questions:
1) Anyone with an OBD-II scanner can give you the codes (I have a PC based OBD-II program myself), and 90% of the time they (or the collective thinking of CEG) can diagnose the problems using the codes. As a metter of fact, CEG has a better track record than most dealerships at solving tough problems. Go to the Group Buy section - the Cougar guys are running a group buy for the scanner a lot of us have ($75). Did the dealership give you the actual code? With that, we could run a BS check on their diagnosis.
2) The big manifold you see under the hood is the upper. There is another intake under that (has fuel injection in it, etc.) that is the lower. I have never done it myself, but I don't imagine it's too difficult, especially if the dealer wants $220 (about 3-4 hours standard labor).
Welcome to CEG. Where in Philly are you?