I helped do an '01 Cobra crate motor swap into a 97 GT. It was less hassle than we expected. Basicly, we just used everything from the GT to run the Cobra motor including the GT PCM. We had to build our own fuel rails to match up to the return system and change all the connector ends to match the new style Cobra injectors. Then we had a custom chip burned from JMS. Runs flawless! I'll bet your current auto trans will bolt right up. You might have to dig up an 8 bolt flexplate, I think all the 99 and newer 4.6's had an 8 bolt crank.