I've owned a few bikes with inexpensive suspension parts. Most of those would be damper rod forks. I've never had one just start making a clunk noise over bumps. If I did, I'd never just live with it. Forks are too important not to fix. The Versys fork parts are reasonably priced as well, so if it were the forks, no excuses.
Clunks from the brake calipers, forks, and triple clamps would all be felt through the handlebars. That should be your first indicator. After verifying the caliper mount bolts are indeed torqued, then vigorously pumping the front end up and down with the front brake applied would be the first way to replicate. Getting the front wheel off the ground is also another good check. Have a friend pull the weight of the bike onto the side stand and rear wheel. With the front off the deck, grab the forks and start shaking. If there's any movement, then you need to retorque the steering head. If you've been clunking for awhile your races are probably dented, in which case you replace the steering head bearings.
If that aint the problem, then go on a ride over some potholes or sharp edged bumps so the front end has to react with high speed damping. If it clunks then you may have fork problems. It is possible the damper cartridges are loose and smacking the fork bottoms, though this is unlikely, as you would also have a high probablility of fork oil leeking out the bottom of the fork. The other fork possibility is the bushings are worn and you have considerable clearance between the fork tube and slider, though this is also usually preceded by oil getting past the seals. Really though, unless somebody has recently been into the forks and reassembled them incorrectly, there's not much reason for the forks to get noisy.
Another option particular to the Versys is the handlebar mount itself. Check that all four bolts are tight against the upper triple clamp. Again, you'd think you'd feel that clunk in the handbars.
Now, tell us what the real problem was.