I would say check the u joint and drive shaft splines.
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There is some history of early failure of driven spline bearings. There are two 6905 bearings pressed in side-by-side in the driven spline and you can only feel the outboard one with the wheel removed. The spline has to be removed to examine the inner bearing. I had the inboard one go bad and it did cause a clunking sound when the bike was run in gear on the centerstand. Mine lasted a good many thousand miles but some are found bad very early.
I think the trick will be getting my dealer to accept outside suggestions, but I'm going to try! Hopefully they come up with something and get my ride fixed!
Thanks for the suggestions!