Try it on a stand to see if you can reproduce it. Might help you isolate it. Doubt it is the rotor, no more likely than the belt drive sleds anyway. I would check chain-case tension first, easy to do (if you don't know how, it should be in the owners manual how to do it, or just ask if you need to). You can check the filler plug (magnetic) for particulate but I pretty much guarantee you will find some, that is what the magnet is for. Could not hurt to open up the chaincase, check the condition of the internals, check the tensioner (had them break before). Clean it all out and put in fresh oil. But that is a bit more of a chore.
I just picked up a 17 Axys with a chaincase, switched out tracks, and under certain conditions, low speed and off-throttle, I am getting loud clicking / vibration, I figured out it was the clips slapping / snapping against the hyfax under certain conditions. Center driver appears to be not on center and was rubbing hard on one side of the center punched windows. Talked to friend of mine at the dealer and a mechanic happened by, turns out the center driver can drift slightly off center. Check if that is the case... if it is they told me you can carefully drive the center driver back to center with a little persuasion... equally on each side of the center driver...
