As a follow up I was wrong about my crank being out of true. Had it checked today with a dail indicator mounted on a lathe and it's just about dead on true and very much within spec. I also was told that having my counter balancer gear off by the thickness of the scribe line is not an issue at all. So either I just forgot how much these things vibrate or I'm just looking for problems. It might just be that the bike has higher compression now with the new old stock cylinder, it does seem to make a tad more power and have a little more crack to the exhaust note. Also perhaps contributing to the vibration is I've been running it more conservatively not quite going passed 8k or so. It actually seems to get smoother more towards red line 9-10k so maybe once I'm fully comfortable with break-in and run it hard it will actually seem smoother.