I don't see a "non-machine shop" way of solving this problem, unfortunately. From the installation instructions and the picture on the Scotts website, it looks like the damper mounting bracket is supposed to sit flush on top of the top clamp, but your VFR's top clamp is not flat. Assuming the raised surface would be able to adequately support that bracket, yes, a machinist should be able to turn an extended nut (with the groove) which would allow the damper mounting bracket to sit flush on top of the top clamp. You might also need to raise the tank flange bracket to match the new position of the top clamp bracket, but that should only require some alloy spacers of the correct thickness.
(You might also ask Scotts why they didn't make one for this model, considering they've had 10+ years to do so...)
For the new custom steering stem nut, I would probably choose stainless as the material, but I'm not the one who has to work it! Good luck.
Ciao,
JZH