sounds like it could be a starter drive stuck out and not disengaging,check to make sure it moves freely,now would be a good time to do it,since you already have the oil out.make sure the armature shaft isn't crooked or bent and check the bushings for wear.i say these things because ,they are simple to check and you mentioned the PO had only one bolt in the starter,and may have done some damage.Another possibility is your rotor could be rubbing the stator slightly.I remember a couple of years back some one had some difficulty getting a rotor to align correctly,although I can't remember who or why.Calling upon all my senior members:
'just finished rebuilding my whole engine; cracked case; replaced stripped shift shaft; cracked/corroded dampers; almost every single gasket, Orings, circlips; replaced thermostat with new/used housing. I studied/researched fellow member's "Roach" videos (I owe that man MY LIFE!) and my manual and was very careful to avoid mistakes.
Once reassembled, I poured in coolant and immediately leaked through right side chomed pipe (upper part of pipe where cyls meet). I realized the new Orings where not in all the way; they were pinched. I removed right exhaust; subframe, brake; big/inner clutch cover to redo that pipe with new Orings and destroyed that big clutch cover water gasket in the process. (presently awaiting new one); Bummer.
Before this removal, (mentioned above) and as the leak was so small, I added three quarts of oil and fired her up. Everything sounded magnificent (no more HLA taps, no skips; magnificent!) but... there was a whirl sound up front/right. What is that??? I inspected the inside (when fixing the Orings mentioned above) and everything looked good. As it appeared to come from around the starter area/right side, I thought it was the washer that floats over the idle sprocket (that connects to starter/balancer) but didn't see any aberrations. I assembled everything with a good engine rebuild lube (it's black with moly). I was extremely cautious and attentive with this project. I was so certain that although I stripped her down to bare bolts, she would start immediately once assembled and her float bowls were full, and she did!
But what is this whirl?!!! Please let this be some kind of breaking in process that will disappear after a mile or two. Maybe just the starter?? Upon removal, the prior owner only had one bolt holding it on. Removal of it was difficult as it was gunked up with dried oil/sludged nastiness/ had to use rubber mallet. I cleaned her good and upon reassembling, she went in nice and smooth. Could this be the whirl? I can accept a new/used one But how can I tell? Soon my gasket will arrive, then it's back to this whirl... What is it?
Any and all solutions and/or possibilities will be accepted. Ride safe.