I built a harness that plugs into the 3rd connector on the NAOMI PSU (the smaller one that doesn't connect to the NAOMI directly) and from that I added wires and connectors for both the JVS I/O board and the Gun board.How are you powering up the Gun Sense Board between consoles
I don't think you'd have any problem tapping power from the JVS I/O 12V output header. I believe some of the Gun games uses a dedicated 12V supply for the gun board. This is just speculation but I wouldn't be surprised if that was done simply to keep voltages fluctuation from the rest of the hardware from effecting the adjustments/calibration of the gun hardware.
Back in the day when I was an arcade tech part of our standard procedure with calibrating gun games was to first dial in the power supply because variations in the voltage could screw up the gun calibration as well as the guns ability to track at all.