May not be your issue, but in my case I got lucky that factory screwed up twice, one that was easy to find which lead to finding the other bigger issue.
At around 137 miles on my Limited, I developed a leak. Turned out to be the o-ring around the starter shaft was 1/2 missing (installed incorrectly, probably pinched and the other 1/2 blew out). When they pulled my primary to diagnose, they also found that my compensator (the new SE version) was not installed correctly. Looked like it had about 100k miles on it.
In any event, before they replaced the compensator I had terrible shifting issues. On decel to a stop, I would get a horrible vibration/hesitation that would just shake the hell out of my right bar similar to what your describing.
I thought it was me. I'm not used to the bike, maybe it had something to do with the ABS, maybe it was the damn stock setup and stock tune, maybe this is just how a bagger idles -- you get the idea. The vibration though, was still apparent when at a stop with the clutch pulled in. I was going to ask them about it, but got the leak before I got over to them to inquire.
Anyway, when they replaced the compensator, the symptoms disappeared, man I though I had a brand new bike -- wait it was a brand new bike.
