Managed to eliminate the vibration I was feeling, must have been in the back end. It went away after I replaced the chain. The old one was stretched to it's limit.
I've noticed that when the bike is cold, it seems kinda boggy until I hit 4500 RPM, then it just takes off. It gets better as the bike warms up, but today it didn't seem to go away. Now it is very cool today, 5C or 41F, so maybe it didn't ever get warm enough. Is this a jetting issue? I am running stock sizes. The bike has the stock airbox, but it is a 2 -1 exhaust.