From your description it's hard for me to tell what the problem is. In your first and second posts, you described the T.C. lock-up problem perfectly. Now you have a problem when the car is at idle? That sounds like a separate issue. Make sure the air filter housing is installed correctly. If it doesn't fit properly around the MAF sensor it can cause exactly the problem you've just described. I've seen this happen many, many times.

To answer your question about the fuel filter being clogged? Sure it's possible. The diaphragm pressure regulator may have failed too, but I don't think it's what's causing your "miss while shifting" problem.

The above mentioned items are easily checked if you have the right equipment (fuel pressure guage, MityVac pump, SDS). Anything else is just a guessing game. At this point I really think you need to get back down to your dealer and go for a road test with the Shop Foreman. They shouldn't have a problem with it, and it shouldn't cost anything. I do it all the time. Also, you never told us the production date and manufacturer of the radiator.