In the end I doused the shock with silicon spray. Whether the plastic guard for the chrome shaft was rubbing on something, or whether the spring was rubbing on something as it compressed (ofc the coils tighten as they compress, so could be on the mounting surfaces?) that finally cured the noise!
My box of bits arrived from Germany today, so I set about fitting the replacement airbox.
As part of that I had planned to take off the throttle body for a clean, as it's had oil caking on it for a while. As far as I can tell that's due to the previous owner over-filling the oil. Excess oil makes its way into the airbox through the crankcase venting system, and from there any which doesn't pool in the airbox goes out through the engine The broken and therefore loose-fitting airbox had (I guess) let some of that get to the outside of the throttle body, and it was thick with it. No pics unfortunately, but hopefully you can imagine a dirty Del Orto throttle body and a shiny one.
I also removed the IACV. Before: After: I had wanted to replace the plugs but a) I only have 14mm and 19mm long plug sockets and b) Gordon's sold me plugs for the F"650" twin instead of the G650 single. So, that goes back on the list of "some day". Not urgent though, as the bike really runs great already.
