Sorry, but the T45 is better than the 3650. A lot of 01 Cobra guys have been getting rid of their 3650s and getting T45s from D&D. I went through 3 3650s before my warranty was finally up, then I got a TKO. The 3650 is garbage and you can't even rebuild the pieces of crap unless you want to pay Ford far too much money for the parts. Tremec doesn't even sell them! And the difference between the 31 spline setup and the 28 spline setup is negligible since similar setups result in broken half-shafts.
I would still get an 01 since they are newer and, only IMO, look better and have better seats.
Just to remind everyone, the 3650 is garbage. Garbage garbage garbage. :-D