Good chance it is the Alum, Triple Tree Stem- "Clunk" issue.
Loose forks feeling
not a recall but a service bulletin with a new Flanged nut that torques down better on the Aluminum Triple Tree Stem/
My 06 D still needed it when I got it in 2016 -
Like a slow speed "clunk" - WTH was that?
Can wear the Fork bearings out...
I got a Harley Shop to do it they did the needed fallway adjustment also
$100. parts and labor.
I put 2 new front rotors and pads afterwards Cured it.
"IF" that is the case:
The loose forks add to imperfections and issues with the rotors/pads.
Maybe upgrading to the Flanged Nut, scuffing the Rotors with a scotch brite pad, and bleed and fill might get clear it up. Pads are probably beat up some from the "bouncing/Clunking? so replacing a good idea.
* SERVICE BULLETIN M-1215 STEERING STEM NUT KIT-
06-08 VRSC Models with Aluminum Triple Tree Stem
new flanged nut 8193 kit 45736-07