Im a repair guy by trade so dont get me wrong boys its just a little disheartning to have sutch a cool ride being undependable right off the bat. The reason I chose this paticular Valk. was because I new the old owner personaly and he does try to take good care of his toys and he assures me his local Honda shop did all his maint. Still I havent seen any grease where it should be and no o-rings on the rear wheel thus the final drive failure. Anyways back to this clicking on the rear breaks, you can also feel the clicks but only when you apply the rear break. Is it possible that one of the calipers is sticking and the other caliper frcing the pad into the rotor cooling holes?
There is only one caliper for the rear brake. If the pistons are misaligned you should be able to see that by looking at the caliper, brake disk and checking the pads.
When you had the wheel off did you check the bearings? When the rear end was put back together, was it done right or just done? I made a slide show (its in shop talk) that shows the right steps.....its call chrisj's rear end service
From my personal experience the brakes are seldom the problem....sometimes the springs holding the pads in are loose and that can cause some noise...I have seen pistons stuck so uneven pressure cause some problems....generally those are obvious (if you look close) and easy to fix.
The noise you describe sound more like a wheel bearing rather than the brake
