I had the same questions when I was reassembling. Apparently the bottom ends on these bikes are pretty bullet proof. Your shells haven't been starved of oil, so they should be good to go. Any minor imperfections can apparently help hold oil, and aren't to much to be concerned about when clearances are within spec, as long as the crankshaft journals also look OK.
Are you going to check the clearances on the rods too?
If you've got an air compressor, blow that bearing out, if there's any notching, or any lateral play, replace it.
My shaft and bearing came out as one.
To get the starter clutch back on, you have to carefully and gently rotate&angle it until you get the splines to line up, it takes a little bit of patience.