...BUT, big BUT, I still have the clunk! I retorqued the bearings twice, the last time using figures from a number of folks who have done the tapered bearings. Still there. I lifted the front and shook the forks/wheel assembly and there is no play. But the clunk is there when I lock the brake and pump the suspension. I don't think it is as bad as it was before but now I'm fairly sure it is not the steering head bearings.
...
Are you sure that clunk isn't your floating rotors bumping into something? ...
Happens on all three of my FJRs.
Put the bike on its centre stand, sit on the ground facing the front wheel, grasp the brake disk with both hands as if it's a car steering wheel. Now rapidly turn the
steering-wheel disk too and fro, see if you can hear the clunk. Repeat for the other side.
The "front brake on, push and pull on the handlebars" test would do the same thing to the brake rotors, it can't really tell the difference between brake rotor float (which is totally harmless) and bad steering bearings (which isn't harmless), they sound and feel very similar.
For steering bearings, put the bike on its centre stand, stick the wife on the back or jack up under the headers (with a wooden platform to spread the load) so that the front wheel is off the ground. Sit in front of the bike, grasp both forks, push and pull the forks. If your can hear/feel any play, that's your steering bearing (or your forks are b*gg*r*d).
I have to use the "jack up under the headers" method, my wife doesn't weigh enough to lift the front.
I add this in case she ever reads this and justifyably takes offence.