You need to split the power into two distinct groups. One being control power, the other being motion power.

Control power you generally want to remain permanently on, and powers things like the controller, input sensors, buttons, etc. Basically anything that being still active isn't going to cause motion.

Motion power is anything that powers things that move i.e. stepper drives, spindles, solenoids. Motion power you want to kill as quickly as practical in the event of an E-stop.

If you don't want to go to the expense of using a higher voltage for controls, use a 5V version of the relay I linked to previously, and do what Jazz said to create a latch. That way you can use the contact that's providing the latch, to also control the E-stop input on the BOB.