It looks like repeatability is what you need, not accuracy which is good as even a poor quality screw will still be very repeatable.
Maybe make it so that you can easily put the base panel back on the machine to take a tiny bit off untill it fits?

Surely you would plane the proud part down, not sand it. Shouldn't take long to plane off a mm or so.

Have you considered making a complete CNC router ... then you can make it cut the holes rebates etc automatically.