This is an application where formulas would actrually work pretty well, since the transform is pretty simple, especially if the misalignment is only in one axis. For example, if the part is tilted down by 0.010"/inch as you move in Y-, you just add a formula for Z that is a linear function of Y (assuming your Z=0 is set at Y=0):
F(x) = x
F(y) = y
F(z) = Z + (0.010 * Y)
Though you're still FAR better off simply getting the thing trued up to begin with....
Regards,
Ray L.