I am in the middle of having a cobra motor installed in my GT and everything seems to be ok...although I don't have a computer for it. The engine was supposed to come with the ECU and didn't. But is it even necessary? Can the GT one be re-programmed?
It's easier with the computer, but we've done tons of chips and Xcal 2's for 4 valve Cobra motors in GT's with the original 2v motor. There's a lot you have to change, but they usually work really well. If it's a Cobra motor with knock sensors, you'll probably lose those, but that's about it. Ther biggest thing is that the two motors have the same type of ignition.