Dave you do realise you can jog machine to any where on the table between tool changes. You don't have to have the G-code do it.?

Regards the Bed then shim it tooling plate. Thou I think you'll find you may end up using a spoil board more than you think. For anything other than precision jobs that must have perfectly flat surface it's much easier to screw or stick material down into something like MDF or Ply. Clamps are ok but they don't always suit the job so what do you do then when can't clamp or find hole in Matrix of holes.?