If it's metal to metal, and you tear it down, you should see a shiny spot/metal upset, or a deformation, where it's connecting/colliding. Have you jacked up the back of the bike, applied the brake, rotated the R. wheel by hand and tried to replicate the problem? The caliper bracket would be my first suspect, perhaps the anti rotation lug is getting worn, it is Aluminum against steel. Bottom line, things shouldn't be clunking whatsoever back there, but you already know that.
