It's gotta be the brakes. The only way to make it clunk is to hit the brake, the real brake, as it doesn't clunk if you stop with just the parking brake. It does squeak pretty good though.
I'm going to dig into the front calipers again tonight. Will post up a pic, just in case I'm not seeing anything obvious... appreciate the help!
82 fj40, 99 uzj100, 06 gx470
97 DR650, 05 525EXC, 01 XT225, 09 TTR125, 07 TTR90, 07 CRF50