I had the same issue on my 2011 R3R, and it was driving me nuts. After a great deal of hunting, it turned out to be the chrome tip on the front fender that was making the noise. The engine vibration / wind / road vibration, a specific speeds / rpms would cause it to rattle... Once discovered, I removed the tip, used a small piece of felt as a pad, and then reinstalled it... It was an inexpensive invisible fix and the problem was solved...
Just my .02
B