At this point, we decided to forge on and took the best parts from the two motors, new cam chain and guides, etc., and made one, fresh, zero mile motor.
We just got her back a couple of days ago. She has a tiny puff of smoke from time to time while the rings are still seating (only about 50 miles on it so far), but runs stronger, better and quieter than ever before.
The stock exhaust looks and sounds great.