It's been a while and I can't remember the full differences but I can see at least a few just by looking at the picture of the RS loom, maybe you can tell me.
Power - Mine were fully wired for -5v, 5v and 12v (+GND) with multiple 24/0.2 main power wires and additional 16/0.2 auxiliary wires. I also wired in an additional 9 pin AMP UP for use as a power IO for 5v + 12v power source / monitoring and also the ability to add -5v in via negatron or similar.
Controls - Mine had an inbuilt CPS2/3 kick harness with was 'fully linked' between the 10pin and 12pin AMP UPs and also buttons 4/5 on the JAMMA harness to make JAMMA+ support more seamless. I offered these in a couple of pinout configurations depending on the customers cab they were going into.
Audio - I used a voltage divider circuit (something I would change now) and all metal RCA connectors.
Video - I used a VGA breakout board modded with 220 ohm resistors (IIRC) via Molex KK series connector on the other side of the resistors.
Misc - I used a DPDT switch for the coin mech connection as IIRC there were issues with having both JAMMA and JVS wired in parallel. Using the switch allowed them to be both plugged in and reduce change over time/effort. I also added diodes to the credit/service piggy back loom as there were issues with inputs being held on certain JAMMA boards. I also offered the looms in two lengths to suit both sit down and stand up cabs.
There are probably more but my memory is hazy, as is my beer
