I do not have the answers to all your questions, but there is one big thing that jumps out at me from your post and tells me you really need to research more into this car and how it is set up right now:
A legacy GT cannot run without the intercooler, at least not well. The intercooler connects the air from the turbo to the intake of the engine. Without it there is no way that any air is getting from the turbo into the engine. Maybe there is some additional piping like a fmic or something going on. That is what you need to find out. But I can guarantee you the car is not "running smooth" as you say with no intercooler in place.
EDIT: I saw the pictures in the other thread you posted. That car is indeed missing the intercooler. There is no way that car is running as well as you described, if at all. There would be serious vacuum issues not to mention complete separation of the intake and exhaust circuits.
Last edited by rlefevre; 04-13-2013 at 02:02 PM..