I would probably try to get rid of the pots. If the circuit design really required them, I might use digital pots.
Do you really need both hard limit switches and optical limit switches? (For my Bridgeport clone, I'm going with mechanical limit switches and TBD home switches). It appears that your reasoning is to have the hard limit switches turn off the power and the optical limit switches interface with the micro. But if the code is correct, you should never hit the hard limits -- or any limits for that matter.