I mentioned checking the shaft first mostly because its so easy & just possible if there was any heat created in the machine work it could have caused it to move, especially given that its been heat treated already. Cutting off the front end, the center was lost but it could be chucked at the front diam. & a center put in the rear bore & then indicate the front bearing area.
When that main drive/mainshaft br'g. is shot, its almost a guarantee of a mis-align somewhere. Takes a really hi-torque motor to apply enough gear load to hurt one.
The orig. trans. were very forgiving & would live with a block face not square to the crank or the bellhs'g. faces not parallel or the bock dowels off center. The newer boxes won't tolerate it. Some of the hi-dollar gearbox sellers won't warranty them unless you furnish them four-position indicator pics before installing.
Doug