You shouldn't need to disconnect any wiring in the JAMMA harness itself (the "JAMMA Chart" picture).
I think the two purpley wires on the left are the 120V wires feeding your DC power supply.
Check the labels on the DC power supply itself where the wires attach. I think they say "AC".
You should be able to disconnect those two wires. That will remove the power from the DC power supply.
Where are the two black wires going? I suspect they're going either to your monitor, or the marquee lighting. If that's the case, you'll need to disconnect those wires from the DC power supply and connect them to the hot wires again.
The bottom line is that you want NOTHING connected to the 120V AC screws on the DC power supply.
I'm not sure about the greenish wire next to the purple ones. That should be an earth ground, and leaving it connected shouldn't hurt anything. HOWEVER, that is honestly the worst wiring job I've ever seen, and there appears to be a ground loop between the AC side and the DC side, that might be where the noise was coming from all along. See if disconnecting the two purple wires does the trick. If not, we'll go from there.
Here's how the wiring should look (minus the earth grounds). Just disconnect the AC from the Power Supply.
