Let the transmission input shaft snout be its own alignment fixture- - - -Give the pilot bushing a little clearance so it's a snug slip fit, put a few drops of Loctite on the OD, and install the transmission without the clutch so the bushing self centers while the goop cures. Instant perfect alignment! Loctite says the green stuff will take up .015" of slop. Just be sure the hole in the crank is CLEAN so the Loctite gets a good bond- - - - -and don't get any goop on the ID of the bushing! If you ever need to remove the bushing again, a Propane torch and 500 degrees F. breaks the bond.
Jerry
