Run all 4 +5 (pins C,D,3,4), all 4 Ground (pins A,B,1,2), both -5 (E,5) and both -12 (F,6) wires from the JAMMA harness to the switcher. I've never seen a board that I can think of where the pads weren't common to the appropriate pins in the harness, but I always wire all of them.
I asked about the monitor because I've only ever had two monitors that had a ground (green wire) running in and neither of those required an isolation transformer. RCA may be referring to the tube. If you can take a picture of the monitor chassis (the circuit board), perhaps someone can identify it. Alternatively, check the myriad of stickers and look for a model number (likely starts with WG and includes four numeric digits).
Or you can check
Bob's Monitor ID Page to see if you can match your chassis.