Have you laid a straight edge across the face of the rear spocket above the chain and looked at the run of the links? If a spacer is missing or on the wrong side the run will be at an angle to the face. Frankly, I've been thinking about this ever since your first post and I'm pretty much stumped. No chance the tire is on tread reversed, is there?
I thought: balance, out of round tire (really rare but it happens), bunched up tube, spacers reversed, tread reversed, sprockets out of alignment, possibly the wheel knocked out of true when changing the tire. Then because it was apparent at a certain rpm I thought carbs, balance or mix screw...that could be disproven by revving in neutral, though, so that's probably right out. Any chance the 16 tooth didn't go on straight or isn't tight?
