I have the same problem with my 1998 GS-R. Did you ever figure it out? I am thinking it is either because I have decaying engine mounts (visible)... or a bad clutch (but I installed a new clutch less than a year ago, with a new light aluminum flywheel..I did NOT have the flywheel turned since it was new...didn't think I had to.) It still did the chatter after I changed the clutch, just not as bad..

I don't want to install engine mount inserts... I like a smooth ride also.. I am hoping you figured it out!

Please respond. thanks.