The T45 shares common internal parts with the T56 and shifters with the T5. It also has a splined output shaft. This could make it easier for your application. T-45 History
The 01-04 TR3650 have a splined output and solid mounted shifter. The 05-10 have remote shifters, internal hydraulic slave cylinders, different input shafts, and flanged outputs. TR3650 History
Adjustable Throwout Bearing?
For transmissions originally equipped with cable clutch throwout, it's possible to space the clutch pivot up to 3/8" to improve clutch release distance. Make sure to double-check fork to pressure plate clearance before final assembly. Or use the Mcleod adjustable throwout bearing listed in the parts list. Or try one of these: https://fortesparts.com/product/clutch-fork-pivot-ball-ford-fox-sn95/
Input Shaft Support?
Use a readily available conversion bearing from American Powertrain or similar. You should see a 1.7" OD/0.69" ID dimensions.
External Hydraulic Slave Cylinder?
Modern Driveline offers solutions for both transmissions.