Looks good and sounds good. Will be interesting how the MPG works. I have never been able to get the MPG work well with the SS nor the ESS. I want it to work in Velocity/Step mode like on commercial controls but it neither as responsive nor the step size is correct.
They don't exactly provide this information in the manual, but based on their Active Low setting in Ports and Pins for the limits (on page 20) I think that the inputs are normally pulled high. Changing it to Active High (uncheck the Active Low box) should fix this.
It's OK them being in series like that, but you didn't mention where are you wiring them to. Is it directly to the PP without a breakout board? If so then I think that the PP inputs are being pulled down normally anyway, so you'll need to connect the other side to 5VDC instead of the COM (which I assume is GND in your schematic)