After half heartedly chasing a front end clunk on my 6R for the last few years, it finally got bad enough to worry me....and get me motivated to find it. I was thinking something was wrong with my front forks or steering head bearings. After going through just about everything on the front end of the bike the problem persisted and was becoming more annoying. I finally stumbled onto the problem. The ram air intake duct on a ZX-6R looks like a simple rubber boot that connects the ram air inlet to the the airbox. It's actually a rigid structural member that serves a secondary duty in supporting the fairing. The 6mm mounting screws were just loose enough to creat a small amount of relative motion between the duct and the aluminum steering neck that was being amplified by the the hollow aluminum frame, made a kind of kerthunk noise everytime I hit a bump. I went out looking for big bumps to crash into last night to try and see if I could see or identify the source and sure enough, I finally saw the fairing move about 1/2 inch over a big bump. Tightened all four of the ram duct screws and she's quiet again.
Here's the screws, two on each side of the neck.