When reinstalling the outer primary cover, get a couple bolts about 2" long, cut the heads off, and use as alignment studs. Cover slides right on and gasket in place.
How did your jack shaft gear and ring gear look? My ring gear didn't look that bad until the clutch basket was off and you could look down between the teeth.
My inner primary has two alignment dowels in it, yours didn't?
Funny you ask about the ring gear.
Some time ago I complained about the starter noise we we have been discussing to the dealer, they never heard it. Then during one service I brought in a picture of three pieces of metal I found on the magnet that looked like ring gear teeth. Again they didn't find a problem.
When I pulled the cover off the other day I found four missing teeth on the ring gear, and what was left was worn smooth.
The starter gear looked fine though.