Control Schematic Advice

[EddyCurrent]

I may be wrong but I only wanted the limits to kill the steppers and leave power to all the other systems and the estop to kill everything but the supply to the bob.

There is no right and wrong, that's a fair requirement. I chose to put the limits and E/Stops in series because I couldn't see the point of having both scenarios you mention, what's the point of killing power to the steppers but leaving the VFD running for example ? You can still put the limit override switch across them if they are in series with the E/Stops.