When I mount my T-9 it hit the crossmember. I just raised everything slightly. I put one washer under each motor mount, and 2 washers under the gearbox mount. That gave me enough clearance.
The T-9 is wider than the original T-3, so the cover over the gearbox had to be modified to fit, either pounded out, or cut out. I also had to open up the hole for the gear shift. It was close, but as I remember it sits slightly farther to the rear. No change in propshaft length, just the different yoke.