I agree that 24-pin ATX isn't much better than a regular JAMMA harness in the grand scheme of things when it comes to mechanical issues. I also agree that RJ45 and CAT5e is the way to go for video as it has the bandwidth and cabling is everywhere, plus you have 4x twisted pairs, so each component of RGBS can have it's own dedicated twisted pair and matching ground that goes to the dedicated video ground pin.
I don't think JAMMA ever officially specified anything more than a single speaker at 5W with 8 ohms impedance, right? if so, ohms law says we should be roughly in-spec for 28 AWG IDC on a short run? Putting the speaker wires on the IDC 34 cable should nicely use all 34 available pins.
Power-wise, have you looked into the 8-pin TE MTA-156? It's rated for enough current (orange connector) and should be the easiest thing ever to make cables for with an 18 AWG IDC cable and a punch down tool. There's JST VR as well, but seems rare?
What's the official JAMMA spec for current across +5, +12, and -5 anyways?