The AODE is essentially a 4R70w with the old AOD ratios, it should control it, athough solenoid impendences may be different, TCC for sure. The 94-95 Mustang ECU and 94-95 3.8l Tbird's use the 60 pin OBD I PCMs, if the OP was starting with a 94/5 3.8 car I'd definitely recommend that route. However the 94-97 4.6s all use the 104 pin OBD II PCM, and there's no getting a 60 pin PCM in there without a ton of rewiring.
Ton of good info there.
Ahh, I didn't know that the PCM/ECU connector was different. Your EDIS plan sounds better and better with every post.
Also Mike's explanation about what switching GT40 heads should hopefully give the OP food for thought as well. Considering how much GT40/GT40P heads can be sold for and how cheap decent aluminum heads can be, for a street car I would personally consider the head swap/upgrade as well.
Or zoomies (straight up through the hood). This gets my vote
SCHOENFELD Demolition Derby Headers Small Block Ford P/N 3522 | eBay