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.
I think the auto mach 1 motor uses a 6 bolt crank and the 5 spd one uses the 8 bolt crank.
As much as I wanted to, I didn't do the swap myself. I had it done by professionals. I was overseas be shot at by ragheads at the time and that made it sorta hard to work on my car. Give Don a call at Modular Madness Motorsports, he's the one who did my car. He's a very good guy, very honest and knowledgable. I don't remember the number, but the website is www.modularmadness.com.
The MACH1 motor is identical to the 01 Cobra that why the site still shows 01 cobra .
The only difference is the MACH1 has updated cams and revised heads.
Greg's has the 8 bolt forged crank and all we did was put the 8 bolt flexplate on , rest is straight forward.
Don