I think it will with a new clutch,diff from a t45 and i think youll need a flywheel,I cant remember if the 3650 has has more teeth on the input shaft.Not sure about the output shaft and driveshaft tho.If you dont get a for sure answer here on the forums try talking to promotionperformance,they seem to really know the stuff.
It will bolt right to the motor, and crossmember. The input shafts are both 10 spline. If you look on some websites, they advertise a 10.5" clutch kit for 86-mid 01 Mustang GT's. But that is because they jumped to an 11" clutch in late 01-04. I have an 11" clutch in my 2001 drivetrain that is in my notch and it is still 10 spline. That kit I bought said late 2001 to 04 Mustang GT's. And as you all know the late 01-04 GT's had a 3650, so I believe they are all 10 spline.
i've done this swap in my 99, everything bolts right up, the only issue u will have is the shifters are different. as long as u have the shifter for the 3650 u will be fine. input and output splines are all the same. very simple swap.