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No "clunk" here... solid and smooth even hitting a hard pot hole (as long as you are not bottoming out). I had experienced a "cluck" feel though and found I could feel it somewhat by backing down a hill and hitting the front brakes (only). It turned out to be the head bearings. Important to check those to be sure they are still good and have the proper amount of tension on them I think. Also, make sure your pinch bolts that hold you axle into the bottom of the right fork (in my bike anyway) are in place and properly torqued (with thread locker). That would also account for a "clunk" (a very dangerous clunk as you could lose or cause your front wheel to lock up).
I was also hearing/feeling a clunk on rough roads and hard braking...tried tightening the tank bolts, retorqued the header pipe nuts, replaced the riser bushings and went over everything up front with a fastener on it...still clunked. Finally realized that the tubes were bottoming out. Rebuilt the tubes with an aftermarket kit only to have both seals blow out within 5 miles and did it again with OEM parts, added 3/4 inch spacers, and put in 10W fork oil. No more clunking, no more bottoming out...Still a little too much sag so I am looking at intiminators.
You could also check the lockwasher located under the stem nut of the upper clamp/triple tree. There was a service bulletin issued on that for 2006 models.
If the tank bolt didn't fix the clunk try this. Loosen the lower triple tree pinch bolts, retorque the steering stem bolt, then retighten the lower pinch bolts. May have to hit the lower with a plastic/rubber mallet to loosen the tubes in the lower tree.
If a simple fix was not in the cards put in some new neck bearings. Mine were dry from the factory and I had that problem. New bearings , mucho grease, no clunk (got rid of my squirrly front end as well).
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