My 2012 FLSTSE3 has had this "NOISE" since the very first day, and it is still very annoying after 9500 miles.
I have changed the exhaust to a Bassani 2-1 Road Rage Long, and added Nightrider XiED's to richen up the closed loop. I has helped with the heat issue, and also has increased the torque when riding in higher gears. That being said, I took it to my dealer and ask if one of the PHD techs could take it for a ride and see if it was something to worry about . . . too my amazement they did just that, and then told me is the the "HEAT SHIELDS" on the Bassani, WTF

So I rode it home, took the HS off and guess what, the noise is still there . . .

This is just another reason why I do NOT trust them. I do my own oil changes and tires, which I have had to replaced the rear at 8500 miles WTH.
It is interesting to hear other opinons on the very annoying issue. Guess I will ride it till it breaks. Like others have stated, it runs good

will continue to follow this thread.
WD
Btw- still using Syn3 in all 3