I have a car with this EXACT swap. Took out the t-45 and had a sweet deal on the t3650.
It was a while ago, but to switch the transmissions, you need to custom modify the crossmember (was a PITA, and it still isn't sitting 100%).
They are the exact same length and diameter, and you do NOT need to worry about changing the housing or shortening the driveshaft.
There is one other part needed, the Dallas Mustang EXTENDED RANGE speedcal. It is around $100 and it is made to convert the mechanical signal into an electrical one. You must call them once the car is hooked up with the speedcal and i believe it is Justin that you need to talk to about which switches to turn on after doing a series of tests.
The only issue I am having and have had since before the transmission swap is inoperative cruise control. I checked the actuator switches, they are all great. No fuses blown, new speed control amplifier installed, and nothing. If anyone can give me some guidelines as to what else to check it would be greatly appreciated!