Personally I won't do it, but I have done so in the past. I don't know if the shims are case or through hardened so I've no idea of the safe limit but I'd expect a thou' to be ok. I wouldn't take 5 thou off, mostly because of the time involved !
But if needs must..... use double sided tape to stick the shim to a rubber bung or something similar which you can grip easily. If you have a lathe you could easily turn something up with a shim-sized recess which would make gripping it even easier.
I used a sheet of glass with wet/dry emery paper on top, that used to be the standard method in the olden days for preparing metallographic samples and ensuring they stay flat. As John says, rotate every few passes to keep as flat as possible. If you manage to keep it flat then I'd put that surface against the bucket rather than the valve head - larger load surface.
Brian