Just as an update to this, I'm no further forward.
I found a couple of problems - left muffler had got loose and slipped forward on the header, made no difference to the vibration, breather bolts on the Arlen Ness Big Sucker had come loose, and that accounted for the visual vibration of the air cleaner, but fixing it hasn't helped the vibration.
I changed the compensator to the newer type, which has made a big improvement in starting the bike, but hasn't helped the vibration.
I checked and rechecked the motor mounts, the exhaust bracketry, and for anything caught between the motor and the frame. Nada.
Three other strange things:
1) Oil pressure is a little higher than it used to be
2) Seems to have stopped using any oil
3) On accelerating - this is perfectly reproducible - around 2800-3000 rpm, there are two separate pings, just like the sound of a stone hitting the inside of the front fender.
Power is still fine, but I'm baffled, and worried that this is a scissored crank.....

Jim