Now, put the new (shorter) input shaft back in the tranny. We don't tip it back up to do this (as we have grease holding our needle bearings in). You will have to wiggle the shaft until it goes in. The gears will need to line up. It is not hard at all to do. BUT DON'T FORCE ANYTHING...unless you want to give me a call to figure out what went wrong...
It should just slide right in.