When I first saw this topic, I laughed and thought about what my friend and I have come to call the "jacked-up harness" (as a vauge reference to "JAMMA harness") that Pump It Up uses. I figured that was too crazy specific to be what you have, but indeed you do.
It is not fully JAMMA, but it's pretty close. I'd have to grab my wiring diagram to confirm if it would at least not break things, but you could potentially just get a fingerboard and solder a couple eyelet connectors to both ends to make a "JAMMA gender changer".
Lights are on 3 separate connectors. I don't remember if you have to do anything with them to make the stage IO usable. DDR (which, for hysterical reasons, is almost identical) requires connecting a couple pins together, at minimum.
It is, however, compatible with the newer Mk5/Mk6/Mk9 system units. They didn't change anything but the audio and power wiring between them. Mk3 uses a couple of 0.084" (HDD drive style) connectors from power supplies mounted down in the cabinet. These are found only on the SD, DX, original SX (not the neo-SX) and early GX cabinets. Audio was from a proprietary header on the interposer/EMI filter board into which the jacked-up harness connetors (but a separate connector). I don't remember what Mk5 did, but I think it had an internal power supply being fed 220V (yes, 220V, NOT 120V - make sure you've got the power supply set right if you swap it). Mk6 and newer are basically just small form factor PCs. You feed 220VAC to a TFX formfactor power supply and pull audio off a standard 1/8" stereo plug. If you've got the appropriate audio breakout cables and power supply in the cabinet (you can just use an old PC supply, if you don't), you can freely run Mk3/Mk5/Mk6/Mk9 in the same cabinet.
FWIW, if you need more info, I know basically everything there is to know about the GX and neo-SX. I've also poked around quite a bit in an old SX and some in a DX.