Motorcycle Questions? Ask a Mechanic.
Hi and thank you for your question.
Based on your comment about mainly happening when going over a bump, it sounds like your steering head bearings are out of adjustment. When they get loose, you can hear that clunk. Since I can't hear it or feel it, it is going to be either up to you or find a different mechanic. Perhaps taking it to a franchised dealer if you can't pin point it or the other mechanic is not at a Yamaha dealer, I would urge you to consider that.
One test you can do yourself to see if the steering head is being allowed to shift and cause the clunk would be to sit on the bike and grab the front brakes hard enough to prevent the bike from rolling. Now, place your left hand on the frame between the tank and steering assembly. Position your thumb so it is flat on the frame but the side of your thumb is touching the "cover, ball race". This would be about the same as stuffing your thumb between the bearing race cover and the frame. Now hold your left thumb still as you rock the bike forward by sitting in the seat and pushing it forward with your feet and right hand. You are going to have to give it several good shoves against the breaks and suspension so you can unequivocally determine whether the steering stem is shifting in the frame. If it is, you will feel the movement on the side of your thumb but not on the bottom of your thumb.
Here is a diagram so show you the cover, ball race I was referring to:
Reference #4 is the component I am talking about feeling with the side of your thumb and using the frame as a brace to be able to detect any movement of the steering front and back that is independent of the frame movement.
If you have any more questions, feel free to ask.