do you have trouble shifting through neutral at all? ah low or high revs maybe? if so, could have a bent selector fork. that's an engine out jobby, but not as bad as you may think. Probs cost bout £40 and some gaskets (instant gasket sealant £5).
When did you last change the oil, and what type did you use? Adjust the clutch at the lever and at the clutch behindthe rubber bung? adjust idle speed to advised rpm when warm. Rear Chain tension can also have backlash because of the slack. Other than that, fazers do seem to have clunky gearboxes. Mine has been clunky and ive done 35,000 miles on mine so far. Just wear and tear causes tolerances to change and worn parts dont mate exactly anymore, making noises that dont always sound too good. I have a whine in 3rd gear on my fazer and zx6r. Nothing wrong with it, just the way the gear teeth mate with one another.
Hope this helps. Maybe you could video the clunk and put it on youtube and post the link? if the clunk isnt too violent when riding, id put it down to just the fazer gearbox normal.
Fingers crossed