I try and post as much info as possible to help others figure out issues with there builds. I know I have used the search function and saved myself some headaches. Wayne, there are two measurments on the starter. The first is flywheel to pinion nose clearance. You need to take the nose off the starter and place a shim and new thicker gasket to get it within spec. You also have a starter pinion tooth to flywheel tooth clearance which you check with a pin style feeler gauge. Mine is within spec. I hope not to mess with shims after it's assembled. I used the bike jack to help steady the engine while I was turning it over for the run out readings. I may just be giving you a call AJ. The engine will be going in no later than next weekend.
I did get the pilot bearing issue solved today. I used a center punch and made three indentations every approx 1/8 inch. It actually raises the metal slightly around the indentation. I then coated the inside of the crank snout with red loctite. The pilot bearing went in with plenty of resistance and the loctite was better safe than sorry. I remeasured the bellhousing and found the lowest and highest spot. It is .010 out of spec. I have .014 offset dowels on the way to get my quick time scattershield centered. Part of the issue is that my engine was line bored even though it was a brank new GM block. The offset dowels should get it where it needs to be. Jim and Todd over at Classic Chevy 5 speed are great guys. Highly recommend them.
I still need to get my crossmember modified to a two piece design. It will not go in due to the lower body mounts.