I'm not the expert, but I will tell you what I did with my recent Jamma pickup.
(with power disconnected to the whole cab, of course)
From the power supply, remove all DC voltages +5V, -5V, 12V going towards your jamma harness.
This should be enough. And it appears that the harness would be the only thing affected. Your marquee will still get its AC. I'm not sure about your coin doors, I dont see them in your pic.
As far as the 'details' you want so you can learn, its pretty simple.
1. The jamma board needs DC voltages to operate. Since houses are obviously equipped with AC, you need the power supply to simply create +/- 5V, and 12V from the AC (just like a computer power supply).
2. Your marquee runs from AC, so it is just split off the power cord from you house AC supply.
3. The monitor needs to be isloated from the incoming AC, so it takes your house AC through a isolation transformer. Attaching the monitor to the secondary windings of a transformer seperates (isolates) its power from any noise that may be produced my other potentials on the same line.
4. Your new J-PAC will derive its voltage from the PC it's plugged into. This is why we don't need the DC coming from the power supply in the cab.
5. You could remove the power supply from your cab completely, but would require a little AC line coupling (not too hard), but keeping it in there for a short temr should not hurt anything.
I hope this helps. Let me know if you have any other electronics questions. (I know I got that degree for something

).
-Stobe