Hmmmm................
I have a bit of a clunk, but I just don't worry about it. I think it's always been there to a degree, but I am not even sure about that. While off the ground, I have done the service manual check of trying to move the forks and they felt fine. While at the dealer for valve checks, I had him check and he reported they were fine. I have checked the brake rotors many times in the past - they were fine, but I haven't done it recently and will again.
I think it's fork internals making the noise in my case. Obviously, it can be one of many things, so if you experience the clunk, you need to check various stuff. But I guess my big point is, if you have the clunk and you check the rotors and steering head bearings and they are ok, then who cares about the clunk?
For reference, mine is a 2004 FJR with 146k. Never had the head bearing repacked with grease. Only re-torqued the head bearings once. I did it myself with a borrowed spanner wrench and torqued them to spec. Afterwards, they felt looser than before the re-torque, so I did it again a couple days later and torqued them a little past spec. They have been ok ever since, and that was a LOT of miles ago.
Loose head bearings should eventually result in dimpled bearing races, correct? Which you should be able to feel, right? Well, my steering travel is still smooth.