I used a standard JAMMA wiring harness. They are available on Ebay from vendors like Tornadoterry and TwistedQuarter. You can also get them from all the arcade suppliers including Bob Roberts.
When you convert a cabinet to JAMMA like I did with the Donkey Kong, the idea is that everything is wired through the harness, including the monitor, controls, power, coin door, and speakers. You can still hook the coin door up as you did (and so did I becaue I was lazy). The coin counter won't work without the original power supply because it needs non-standard power (I think 24v, but don't quote me).
I don't remember where the control panel connects to the DK boards, but you still may be able to hook them up that way. If it were me, I'd get a fully populated JAMMA harness and rewire. However, your machine should at least power up and get video and sound without the controls connnected. I would pull that power connector from the old power supply that's connected to the PCB first and see what that does.