Don't know if this will help but ...
Same noise on my FLHTSUSE3 (08 - 42,000 miles) started after the stock compensator went to hell (30,000- 35,000 miles - banging and hard starting). had to call HD customer service to convince them this was NOT normal - ended up replacing with SE Comp.
After this I started noticing a noise that seemed to come from the right side trapdoor bearings, it was most noticeable at operating temperature and in neutral, the noise would disappear when pulling in the clutch ..
Described by various people as a loud Clicking/Ticking/Clanking sound from the trapdoor. When riding a you could hear a loud clanking sound especially between 2500-3000 RPM in 2,3,4th gear.. 5th and 6th were fairly quiet. (though not nearly as quiet as now)
The dealer replaced the trapdoor and all transmission bearings plus the clutch throwout bearing. Noise still present, at this point they figured the transmission is OK and the noise is being transmitted to the right side from the clutch assembly.
They replaced the complete clutch basket assembly. This fixed the noise problem....
Now at 42,000 the bike sounds and runs like it did when young ... No more strange noises, bike is very quiet, clutch works great and the transmission has never shifted better.
All this and still 4 years left on the extended warranty and I've more then covered it's cost ...
if you put a lot of miles on the bike, the extended warranty is a must!!