Can the input shaft bend? And could it prevent the transmission from bolting flush to the engine?

 

Anything is possible. But its aways the clutch and pressure plate not line up when bolted because the alignment tool was not use.

 

Check the Pilot bearing. My 2.5 Ford Courier pilotbearing was oversised and to dit it the pro's hit it to expand and Is suffered to get the gearbox out. Luckily It saw it.

Wondered how they got it in without breaking the bell housing or bending the Pilot shaft.

Good luck.