On mine, I wouldn't call it a rattle, more like a pulsing sound, always around 5000rpm in 3rd, 4th, or 5th.
You might check this thread out: http://www.r3-forums.com/forum/289-yamaha-r3-general-discussion/39609-front-end-noise-changes-speed.html
You might check this thread out: http://www.r3-forums.com/forum/289-yamaha-r3-general-discussion/39609-front-end-noise-changes-speed.html