Well,
I've put around 2k miles on the bike since I bought it. I removed the trans and lubed the splines (trans/clutch splines and all other splines) with Honda Moly 60 before putting a plate on it. That clacking-type noise was present but went away with the clutch pulled. I was sorting out other things on the bike and didn't address it.
I pulled the trans again after I dunno, another thousand miles and re-arranged the clutch components to try to fix my vibration issue. Relubed the splines and reassembled. Clacking that goes away when the clutch is pulled still present.
Last weekend I pulled the trans again to replace the clutch disc as I noticed the condition of the clutch disc splines when I pulled it to sort out the vibration. New disc, lubed splines, reassembled, and now the noise is almost gone. I can post a new video tomorrow if you guys think it'll be of some use. Note: vibration still present even though I messed with the component arrangement again. I have a NEW clutch cover, NEW pressure plate, and a good, used clutch housing that just came though ebay that I will be installing this Sunday).
Note: in no way am I trying to argue or troll or anything, just report my findings on this clacking noise.
I can see how it can be the alternator "monkey nuts" but mine are new and I've removed and reinstalled the alternator at least 5 times since then with no change. Did not see damage to the "cup" of the alternator nor the drive "fins" so I feel that nuts are properly installed.