Pop off the clutch side cover and check your counter balancer marks and make sure it's all lined up! Counter balancer, crank end, and crank gear all have punch marks. Case marks are more like pointers cast into them. Very important make sure your tach gear cluster stays pushed all the way in when you turn the assembly to check alignement. I found that if the tach gear backs out a tad while the cover is off the gears can drift around and the alignment change even though all the gears will appear to rotate. The tach gear is an odd assembly that also takes up any lash in the system, but if it backs out even an 1/8-1/4" the tach gears can free wheel and make the counter balancer get off alignment. Point is keep all the gears pressed in tight to keep it all meshed properly like if the cover was ON during your checks perhaps do it with the bike layed on it's side.
Probably best to pull out the cylinder head to frame mounting bolt before you torque it back up. After I put about 150 miles on mine I loosened the head and retorqued, but it was probably a mistake that I didn't loosen the frame bolt at the head it might have pulled it off center as I retightened. So for now on I'm probably only going to torque the head/cylinder assembly with the pipe, carb, and frame mount free of it just to be sure nothing is pulling it off center.
Now that I reinstalled my crank (and did who knows what) the bike is smoother and just has a resonance of vibration right at 8k or so, below or above that it smooths back out. I can't say it's an electric type level of smooth but it's not bad at all now and is as smooth as it was before I rebuilt it.
Next time we ride we can compare bikes and see how they compare vibration wise.