You could just make your own cable to replace it, or if you're handy and you want to ensure cleaner power to the board all you need to do is get a newer power supply that has 12V, 5V, (and GND of course) and run it into the appropriate wires on the MPU board.
From the top down the pins are
For my bench, I have JENTEC JTA0512 but you can use any power supply that has enough current. This one has 3 Amps at 5V and 3 Amps at 12V.
I just tie both of the 5V lines on this unit to all 3 5V inputs. The same goes for the GND wires. You need to connect all six on the MPU board to allow all of the current to get through without overheating.
I did try power supplies with lesser current ratings, but they don't have enough to keep everything running on the bench.
For an in-game installation, you'll have to find out what the current requirements are to be sure you have a good enough power supply.
Anyway, some ideas at least
Hope this helps you get started in some way