ok, well, let me repeat, the 3650 sucks. I had three. One just randomly died in traffic... After being in my for less than a month in late December. I never got to race with that one since it was off season. It's a poorly designed transmission. Go to the 4.6 Tech forum and look at their 3650 thread. These transmissions are heavy, inefficient, and break easily. It can barely take stock torque (TORQUE! something we barely have in the first place!) from our cars. Add an X-pipe and race on a cold day and BOOM, there goes second... Plus, the input shaft is the same garbage that came with the T-45. It wouldn't cost much for Ford to put strong trannies on our cars. Oh wait, they did. 2003 got a T-56 that can barely handle the power they put out...
Also, the 3650 came out in mid 2001MY. So, the early GTs (made in 2000 but part of the early 2001MY) got T-45s. Starting in mid-2001MY production run (beginning of 2001) the 3650s were put into the Cobra and the GT. I have heard there are different versions, but they all seem to break in the same places on closely powered cars (modded GT, Bullitt and Cobra).