I know about the "autoleveller" software that will probe the surface of a piece of work and modify gcode so that depths are accurately referenced to the real surface of the work and not where the surface should be.

Is there an equivalent that anyone's written (Mach3 add-on?) that would do the equivalent for second-operation work? Clamp the work down without needing too much care, probe a few reference points, and then modify the toolpath to allow for misalignment (mainly rotation, I guess). After all, with CNC machines, we don't really need to align work with a fixed table axis in the same way as with manual machines (he says, having been clocking bits of aluminium plate this evening for coordinate drilling hole patterns).