Hi MadTooler,
I think it is best to keep High Voltage Motor Power off while +5V for KFLOP/SnapAmp/Kanalog is off. I think that makes most sense and is safer. In other words:
To Power up - Turn on +5V fo KFLOP/SnapAmp/Kanalog then turn on High Voltage
To Power Down - Turn off High Voltage then Turn off +5V fo KFLOP/SnapAmp/Kanalog
It should be ok to have High Voltage on while KFLOP/SnapAmp/Kanalog. But given the option the above method is preferred.
Note Kanalog Outputs power up in an undefined state until after KFLOP boots up. Kanalog has a single relay driver output called SWE that is guaranteed to come on only after KFLOP is fully booted up and all Kanalog outputs have been initialized off. So you might use that to control your High Voltage Motor/Drive Supplies. This will guarantee the High Voltage comes on after KFLOP receives +5V and boots up.
HTH
Regards