Been there, did this to my car.

Swap the flex plate so the bolt pattern matches the torque converter. (balance is a touch different, but not enough to cause any issues)
Have the pcm tuned for the 2.93's vs the 3.29's that were in the GT if you throw codes
And I'd tune the pcm for the difference in load based on the gear change as well.

Overall it's quick and easy.