Either the thrust washer is out of shape or one or more of the clutch plates have burs on them and are fighting with the anti rumble spring and pressure plate, I had this on a Kawasaki once and it was down to a crap quality thrust washer from manufacture, didn't cause any problems other than the noise, if it was a car it would be an indication of imminent thrust bearing failure but I have never seen a real thrust bearing in a bike. If the changes were very notchy as well as the rumble then it would be the clutch plates, the edges of the plates sometimes have burrs on them that cause the clutch to bind slightly during gear changes, these burrs can be removed by hand with a light file, sometimes they stop the plates from seating against each other properly and this can cause clutch slip or rumble.
Yes, I do most of my own maintenance, no, I do not want to do yours. Also the R3 clutch looks like a right pig to get to.
