I was thinking it might be something to do with the flywheel only because I sheared off the woodruff key back in May due to the flywheel not being torqued down enough (long story short-- performed field surgery on stator, didn't have a torque wrench on me, keep riding).

I don't think the punches could be misaligned only because over the summer when I replaced all the seals I missed the third punch and the bike vibrated like hell. I did notice some grooving on the clutch basket which I filed down.

What has me confused is the regular interval of the vibration and the fact that it went away after I shut off and restarted the bike. Not sure if it's relevant, but about ten minutes before the vibrations began I started to run out of gas before I switched the petcock to reserve.

I'm just hoping I don't have to do too much tearing into the engine, I was hoping to make it out to the dunes on Thanksgiving.