Has anyone machined a bit off the clutch thrust bush to give a bit of clearance,for annoying hard to set up clutches?
Yes.
More than once but not for the reason of standard clutches, but the principle applies. I also made up a little bolt in 'cap' so that a non GP cover could use the GP bush. What a tw*t I was! Probably still am, but now I try to use the spigotted clutch centre/bored cluster combination whenever I can. It is by far the best combination to aid clutches clearing fully to avoid broken teeth on first gear.
However, thicker crankcase gaskets work well (CamLam's last forever) & the kickstart engagement is something I've fiddled with as well in the past. Lengthened the slot, fitted a longer, stronger spring. That was to suit an old school six plate clutch with a SII cover & the kickstart shaft moved outboard to suit by cutting back the inner face.
Eventually that cover started to crack but I added steel reinforcement rings shrunk on & all was fine again.