T56 input shaft trimming

About a 1/4 inch more than the gap between the trans case and the bell housing.
You can cut it off with almost anything,(hack saw, cut off wheel, hand grinder)

You want to taper the sharp edges also at aprox 45 degress, so I would grease the input shaft and slide it in as far as it will go into the pilot and pull it back out to make sure you have plenty of shaft there.
(just to help verify that you will still be all the way into the pilot after the cut.)
Polish any surfaces on the input shaft that are not nice and smooth.

Lithium grease the splines lightly (oppinions vary on this), as well as the pilot (I like to fill the crank pilot hole behind the bushing about 1/3 of the way)
Too much and the shaft won't want to go in all the way.