Rough running

probably the crankshaft was never pressed fully into the flywheel.
consider replacing the whole crankshaft/flywheel/connecting rod assembly (or the whole engine if that is beyond your skill level)
 
that's a new one for me, and I'm a repair shop rather than a builder/rider

if that crank was pressed properly, then I'd guess it was sitting too far to that side due maybe to the main bearing on other side getting stuck in the bearing housing and not fully seated in the case

I'd first check that the conn rod is in center of cylinder to see if crank is bad or assembler was really brutal.
 
I had replaced the gasket since I had a new one sitting around. It looks like the new one I put in was significantly thinner than the original... hopefully that's all it was.
 
wrong. that shaft is not normally so close that a thinner gasket will let it hit the cover.
 
Nice. Seems like a good chance to mod the heck out of my engine, since I'll be rebuilding it. But that'll be a project for another day- I've got a car engine to rebuild before I can get to the bike. Thanks for all the help so far!
 

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