Update (this is long)... took the bike to the dealer today. They went over it with a fine tooth comb. Checked everything (spokes, wheels, chain, carb balance, re-torqued engine mounts, etc...). Tech rode it afterwards and said "I can't find anything wrong with it". Well, I paid my bill (why didn't they cover the diagnostic under warranty???) and rode the bike home... still does it. Hands, butt and arms completely numb after about 15 minutes. Still worse between 45 and 65 (its the absolute worst at 65). If you engage the clutch and release the throttle, it's smooth as silk. Engage the clutch and crank the throttle it starts vibrating again.
So, I took it to a acquaintance who is a respected custom builder and asked him to ride the bike then come back and tell me if he noticed anything. He takes off, stays gone awhile, comes back and say's "it starts vibrating at about 50 and gets pretty bad at about 65!". Then I tell him the story about it being checked out, etc... he said, I don't know what to tell you... it absolutely has a vibration. His advice was to run it for a couple of miles in third gear at 60 mph to try and burn out any carbon that may have built up during breakin. Now here is the really interesting part... in third gear at 60/65 it DOESN'T vibrate! Hit forth and fifth and it does! I am REALLY perplexed... could it be something in the transmission???
