I think you are on to something here.
While it's apart, i would check to see if the bell housing big hole is in the center in relation to the pilot bearing.
If it isn't, this could cause a side load on the input shaft causing it to bind.
You can get offset dowel pins for the back of the block if this is the issue to correct this.
Did you check to see if the clutch disc moved smoothly on the splines of the input shaft?
Does it go through all of the gears properly when the engine isn't running?
These are some things i would try.
Good luck and let us know how it goes.