Oh crap... just came back from the garage and the bike won't start.... dead battery never put a charger on before, but unlike this year, I usually start the bike 3-4 times per winter, just to hear the sound !!!
Ok, definitely not convinced the clunk comes from the swing arm.... on the stand, rocked the bike from left to right, and the clunk I hear is the shock that clunks at full extension... I know cause I just removed it and the sound ain't there with it removed. It's those 11 inch Far shocks that specialize on Harleys.... They don't have upward travel like the stock shocks !!! therfore when you rock the bike, the shock goes down a bit and then clunks when it reaches full extension.
I know exactly what clunk you mean, once per revolution only when backing up... Had it for a while last year. It's the brakes for sure !!!! completely went away after I installed Glen's down under bracket !?! I think it's the pads sticking at a specific point on the rotor and clunking when it reaches that point, or the pad holders are bent a little and allow movement.... It's vague, but I'm sure your clunk is the brakes.