When I got my cabinet it had been converted to Tekken 3. The board is fried, but the only connectors used were the two edge connectors (JAMMA and the kick harness).
I'm not sure what that connector is for, but it's nothing to do with hooking it up to the cabinet. You might check out the manuals for some other Namco System12 games. Here's a good list:
http://www.system16.com/hardware.php?id=535Since System12 was designed to be a base hardware for many games (it's playstation-based), it may just be an auxillary connector that wasn't used for Tekken 3.
My Mr Driller 2 (system10) PCB also has this connector, but it isn't used on it either.