Input shaft bent? Any metal shaving on piolt, clutch disk splines or input shaft?
Something seems amiss here. I would leave it apart and cogitate, measure, cogitate, repeat.
This tranny was mated to that engine before and moving, correct?
Starter gear moves freely? The nose of the starter does not show scraches? Fly wheel the same?
You have such a big bind that it really dose not seem that it would be just a tight fit of the input shaft. Did the tranny and engine mate up together with out much trouble?
Did the alignment of the tranny and engine cause a bind on any other parts of the drive line, check Ujoints.