The JAMMA harness connector will work, but the kick harness between MK1 and MK2 is slightly different on a few pins - this is why the low punch/kick aren't working.
Here's MK1, thus your cabinet connector for MK1:Connector J4 (CPU Board - Extra Buttons on Control Panel)
Use Molex 12 Pin 0.100" Header (2.54mm pitch)
| 1 | N/C
| 2 | N/C
| 3 | N/C
| 4 | 2P Low Punch
| 5 | N/C
| 6 | Key
| 7 | 2P Low Kick
| 8 | N/C
| 9 | 1P Low Punch
| 10 | 1P Low Kick
| 11 | N/C
| 12 | N/C
Here's the MK2 kick harness connector:Connector P5
Use Molex 15 Pin 0.100" Header (2.54mm pitch)
| 1 | N/C
| 2 | N/C
| 3 | N/C
| 4 | N/C
| 5 | N/C
| 6 | N/C
| 7 | Low Punch 1
| 8 | Low Kick 1
| 9 | N/C
| 10 | N/C
| 11 | Low Punch 2
| 12 | Low Kick 2
| 13 | N/C
| 14 | N/C
| 15 | N/C
You can see what you need to do from above pinouts. I personally would build a harness adapter from buying a MK2 kick harness (~$20), then solder on a molex 12-pin 2.54mm pitch male connector (~$1) to the appropriate pins, then have your cabinet connect to this adapter harness. The connector model should be Molex K.K 6373 12-pin:
http://www.newark.com/molex/22-11-2122/wire-board-connector-header-12/dp/81C8221
The MK2 kick harness #7 needs to go to your cabinet connector's #9 pin.
The MK2 kick harness #8 needs to go to your cabinet connector's #10 pin.
The MK2 kick harness #11 needs to go to your cabinet connector's #4 pin.
The MK2 kick harness #12 needs to go to your cabient connector's #7 pin.
You could cut your cabinet's kick harness above the connector and add push-on terminals to be able to swap pins around when you change boards, but I'd prefer to have an adapter made to keep the original cabinet harness unmodified.
