Try reassembling a 10,000 lb tractor, with a 3000 lb engine on a splitting stand. Everything has to be lined up PERFECTLY in order for things to slide together correctly. Do not force things together, at most use MODERATE come-a-long pressure at the most. It should go all the way together before you put in a bolt to hold things together.
I have the best luck installing truck transmissions leaving the tranny in gear. You can apply light come-a-long pressure and turn the output shaft, which will turn the imput shaft and allow the splines to engage the clutch disk. Also, if you are installing a new pilot bearing, make sure it fits on the input shaft. Don't just look at it, try it on the shaft. Also, try the clutch disk on the input shaft. If nothing else, this is a mind game to play on yourself to prove that the tranny HAS to go on since the only things that could impede progress did indeed fit at one time.
