My $0.02 for what it is worth.

Why are you not wiring the stepper enable signals. There is plenty of I/O left over to hook those up. When you press enable on the computer it will lock the steppers in place thus letting you adjust the position of the axis when disabled.

Wiring un-fused power in a cable is not a good idea. If a cable is cut or crushed somehow, you don't want your power to be shorted such that it takes out the whole system. It also helps to reduce EMI noise in the system if your power stays inside the controller box. With regard to limit switches, if you are using NO/NC switches, connect the switch between ground and the input signal. Then use a NC switch so that when you reach the limit the circuit is opened allowing the pullup resister on the ESS to activate the limit signal. This also has the added benefit of activating the limit signal if the cable is disconnected. If you are using PNP/NPN sensors for the limits, at least add a fuse to the power wire and take advantage of the same logic if the cable is disconnected.

With regard to the E-Stop circuit, just cutting power to the system is not the best way to do it. Consider this. The spindle VFD has an internal brake. When the enable rotation signal is cleared the brake is applied to stop the motor fast. If you just pull the power cable the motor will have to coast to a stop. Those seconds will seem like hours with your shirt sleeve wound around the cutter. The goal for the E-Stop is to stop motion. Wire the E-Stop into the BOB so the ESS can do what it is supposed to do to stop the system. Also, make sure to apply the cable disconnected logic to the E-Stop. Breaking the cable should stop the system.