I remember one time i had a trans that had a longer input shaft than the original. the trans was rebuilt and the guy replaced the input shaft and it was longer and bottomed out. I had to cut about a 1/4 inch off. may not be your case but thats why i suggested mesuring. also make sure the throwout bearing slides over the input shaft completely. another thing to check is how far the clutch goes on the input shaft. do the splines allow the trans to go all the way in or are they stopping the trans from seating. i always found to go back to the easy stuff first. sometimes you start looking to hard and miss the simple things
