The bellhousing is machined for a 4.6L bellhousing. It's also integrated into the trans so you can't replace it. crossmember is different as well.
I had no probs with the 3650 in my '03 GT. Shifted great and held up to all my abuse. I put 70,000 miles on mine without an issue.
I'd rather have a 3650 than a t-5. With a modded 5.0 i always felt you were one bad shift away from grenading the t-5.
Granted rebuilding a t-5 is easy as pie and parts are cheap. A 3650 is a PITA to rebuild and it's tough to get parts