Wiring looks ok, I can see it is work in progress, as you are missing a few components Like Breakers for the main VFD input circuit a main cabinet input power disconnect.
5v sharing is fine but using each Breakout Boards commons as (1) may cause some problems, some Breakout Boards require Isolated Coms so need to know more about the Boards being used
Will these USB Breakout Boards work with Mach4, or do you have a Smooth Stepper, and these are just attached to the Smooth Stepper Board
What is the Breakout Board you are going to use
As for your drive voltage use what is the most convenient if the dc is a filtered supply, then that may be a better option if you have it, the Ac will work fine as well and may be easier to use with just a step-down Transformer
Your EStop circuit as long as you can disable all the Enables and stop all drives this is ok for most machines like yours a safety Relay in the circuit is the best, these are expensive though so most don't use them.