well now that you have the power supply how it is, you might as well keep it that way.
the wiring looks correct at least in the fact that you have black on common, red on +5v and yellow on 12v.
most of these modern boards don't need -5v (orange).
I would however verify that the +5v is adjusted correctly by using a multi meter to check the voltage at the jamma board where the power wires are.
you wanna see something like 5.1, 5.2volts there.