I've run into this a couple times over the years. Have seen an inch or more cut off the end of the input shaft, as it does not appear the depth of the crank drilling was consistent. Chamfer the edge of the input shaft so it goes through the pilot bearing easier. The advice about it not touching the end of the crank is wise.

I assume you used one of the later model pilot bearings that fits into the flange at the end of the crank!