Looking at the confusion in the manual, I decided to do a few mods. The 5V PSU will only power the limit switches and the encoders. I then decided to power the teensy, relay board and the mega from buck converters to get the correct voltage to each which means that they will be permanently powered, but then cut the red wire in the USB cables so they are not powered from the USB. Unfortunately, I have still got to complete the AR3 build, but I have wired it up outside of the control box and it seems to work okay. We will see what happens when it is finally put ino action.