Epoxy sounds a bit too complicated for something so simple and you'd have to confirm the frame was adjusted to make the plane of the rails orthogonal to local gravity or it becomes pointless.
I'd go with the shim and skim. That cannot fail to put the plane of the base parallel in all directions to the plane which the spindle moves which is what you really want and will minimise the thickness of material you need to skim off the final, sacrificial surface.