Just got back from the dealer.....primary chain is fine, has the right amount of play in it.
Two of their experienced engine guys took the bike for a ride. Both came up with the same diagnosis. One thing that I had done while it was apart was to replace the front rubber mount. Also, Zippers doesn't have a map for a stock engine, only with a Zippers 50mm TB. So the engine is going to be pretty rich. They feel that combo of stiff mount, rich, big cam are all contributing to something I'm not used to. They both liked the power the cam made and it isn't nearly as noisy as they thought it would be. The 103" motor jumps around a bit anyway, the cam may be enhancing it.
I feel better that nothing is drastically wrong. The engine guy did warn me beforehand that putting in a new mount could give me more vibration, since the rubber is stiff when new. It 'could' soften up after a while. I noticed that the vibration in the fairing and bars is less while at idle than it was. I asked whether the center bolt could be loosened a few lbs. He suggested trying loosening all 3 bolts on the rubber mount and run the engine. Theory is if the engine is binding on the new mount, running the engine when loose helps center the mount. He hasn't seen this to be very effective when he's tried it.
Next thing is to get the bike tuned. Since it is surely rich, probably making it rougher than I think it is. And maybe the dyno guy could play with some timing in that 4000 rpm range. I'm going to use the mobile dyno guy that owns Cycle Solutions. He'll be in PanamaCityBeach April 28.
Thanks for everyones help.