I had similar "clunk" problem on my jh600: it always happened when I crossed some obstacles in higher speed (over 25 km/h).

I reassembled front end several times trying to figure it out. Then I changed fork oil and it becomes bit better, so after all I was thinking it is related to fork and I gave up after all.

And just about two months ago for some reasons I remove side stand and I found that "clunk" was gone!.. so now I just put piece of rubber pipe over the place of side stand where it is touching motorcycle frame and "clunk" is gone.

So in my case it was just one metal part clunking on the motorcycle frame, nothing related to bearings, wheels, fork etc.