Manual shifts are critical on input shaft alignment to the crank hub pilot bearing, I use the dial indicator much as Pat described. I've found so many block dowel pins out of alignment, it's not even funny!!!! Now they've come out with misalignment pins, used to have to do some creative machine work. Also, I've found that after I set my centerline, I torque (not just tigheten) the bellhousing to block bolts, then recheck the alignment. Occasionally torqueing the bolts can change the alignment!!!! Really crucial to get the alignment right on the soft-lok and multi-disc clutches.....

With all the up and down slop on a converter in the front pump, getting it within .010 probably beats the factory spec by .030!!!!!