Crank pilot concentricity

You really are registering in the wrong place....

Last...if all you are doing is a foo-foo polish job with some emery paper, .006" runout won't make any difference.

Agreed. The pilot bushing just supports the input shaft snout. The input bearing retainer bore on the bell aligns the crank and transmission centerlines.
Polish the crank, then dial indicate the bell and correct that (almost guarantee that’s off) and send it.