I had a loose compensating sprocket on my bike and it made a similar noise. Don't play with it, mine came off and a good thing things didn't lock up or I would have been getting up close and personal with the pavement. Pull your primary and check everything in there. I might also suggest checking your neck bearings, your fork oil, brakes pads making the clunk in the calipers and the rear fork assembly bearings for good measure.

 

took off primary cover today all seems tight inside no movement at all in comp nut. i,m still boggled

 

When you say braking, do you mean normal or during Hard hard braking?

Going over a bump would simulate hard braking (rear wheel is able to lock up in the air) The reason I ask is it sounds like the same problem I'm having as well, only mine is on a 2010 RK. After much debate with the dealership AND a Harley rep, the rep had the final say and claims it's the compensator gear BUT that it was consider a "normal" operating noise. The dealer thinks it's still not right but claims due to the rep being involved they can't warrenty the repair. My service rep. on the sly, said if I purchase the compenator gear of my choice, they would install it no charge to me. In other words, he'll bury it somewhere under the current warranty. I'm just trying to decide which one would be best and give me the least amount of headaches down the road. When I get it done, I let you know if that solved the problem.

 

More than likely the compensator is ramping over, especially after a bump with the brakes on.

 

I had same problem on my 07 Ultra when braking over bumps. The clunk sound like in the primary. My friend told me actually the clunk is from the swing arm. I changed the swing arm rubber bushing and the problem solved.

 

New bike with ABS does it. Old bike without ABS doesn't. Do all of you have ABS? I believe it is the ABS engaging when stopping and the back wheel comes off the ground over a little bump. Haven't heard any other explanations that I think make more sense. By the way my bikes are 1990 FLHS and 2008 FLHTCI.

 

"...i thought too that the rear brakes may be locking up and clunking? when i brake hard with clutch in or out i get a clunk (soinds like a downshift) only seems to come from primary side. i also adjusted the suspension and do not think this is it... checked all bolts on rear for tightness all seems good. the clunk is driving me nuts.."

UPDATE: Changed the Comp gear with a SE Comp used on CVO's and voilà! NO MORE HARD CLUNKS! This too was driving me nuts but this solved it. Now when I hard brake rear only and the ABS kicks in, I get the "grab & release" sensation (I'll assume normal) and a VERY mild click noise coming from the primary side. I can live with that. Good luck!