It needs a separate kick harness for the second set of 3 buttons. Here's a compatible harness:
http://www.jammaboards.com/store/mortal-kombat-killer-instinct-harness/prod_67.html
The kick harness does indeed plug into the player 3 connector on the PCB. The one listed at jammaboards will plug right into it and if there's doubt, it will come with instructions and/or you can find the wiring detail in the KI manual.Sweet. I knew i was missing something. Where does this connect onto the board? where it saya player 3?