My '04 FJR developed a similar clunking sound at about the 5000 mile point, noticeable whenever I hit a slight bump at low speed. Turned out to be a loose outer ring on the right front rotor. Loose enough that I could turn the rivets with my fingers and there was forward, backwards and slight sideways movement of the outer ring. The rotors on the FJR are not full floaters, they are semi-floaters and the outer rings should have zero movement. When I took the bike in to a Yamaha shop, the service manager first tried to tell me that the movement was normal, that the rotor would "tighten up" as I rode it. I told him that was BS, there was no way those rivets that I could turn with my fingers were going to tighten up as I rode the bike. He replaced the rotor under warranty. As an addendum to this problem, about a week after I picked up the bike with the replaced rotor, I discovered that the right caliper unit was loose, the bolts holding the caliper in place were about 1/3 of the way backed out--the tech who put on the new rotor had failed to lock-tite the caliper bolts. The service manager said he was surprised because the rotor warranty work was done by his senior tech, who should have known to lock-tite the caliper bolts. They fixed the problem immediately, altho I'm not sure I'll ever have them do any other service work for me. Not if I have to recheck everything thoroughly afterwards.I make it a practice to check all the brake rotors for tightness when I do an oil and filter change.
Lee in the Mountains of Northern California B)