Got thinking about the parallel port and found this info refering to the gamebox which I assume is a close copy or maybe the same board since they also mention using 2 supplies.
"The Gamebox PCB uses pure DOS-based Windows 98SE OS as the basis for running the DOS-Mame emulator along with front-end DOS program of ArcadeOS to select the different games from a menu screen.
What's really odd is that the Gamebox PCB (and it's other ilk) uses a seperate ATX power supply unit to power it up rather than using your arcade cabinet or Supergun's PSU. Two cooling fans, one on the ATX PSU & the other's on the CPU itself. So when the Gamebox PCB is powered on, there are two cooling fans in operation for the entire duration -- can get noisy indeed. ^_~
Both the joystick and push button functionality are handled by the ZsNES utility program to register the arcade cab's or Supergun's arcade control inputs to register as "pushed" PC keyboard commands. Several various utility programs are included on the built-in HDD to make sure that everything runs without a hitch.
You can even insert a PS/2 based "old styled" PC keyboard directly into the Gamebox PCB to change game settings, arcade screen parameters, etc. (for easy of convienance)."
Now if this is how your 1000 in 1 functions I can see it not being too hard to get the jamma board portion of it to work. The Zsnes program may just be a ref to ppjoy which was used with zsnes and the code for ArcadeOS is available so it should be possible to see what they customized to make their system function.