Sorry, my harness was for a JOYPAD hack.
<PSXPAD>---<ATX 20-pin connector><ATX other 20-pin connector>---<JAMMA fingerboard>
I now realize you meant a harness for Mini-Pac only, and that the first half of my post was irrelevant my plan was for something else entirely.
Now that I have actually took the time to see what you are working with, here is what I would probably try:
connect one of these to your Mini-Pac pin header.
SCSI internal to external brackets (ebay)install it through the side of your control box module, and attach a SCSI cable from the box to the controller of choice, each of which could also house an identical connector. The connector inside the controllers could be connected via pin headers on strip-board, or, if you find long enough pin headers;
Female SCSI connector>PINS<Female IDE connector of an IDE cable>----<switches
BTW, the only issues I would worry about for long ribbon cables is physical strength or breakage.
I was about to suggest a solution involving an IDE to centronics adapter, a parallel printer cable, and a female DB25, because you wouldn't be using all 40 I/O's at once, but then I realized you would be different ones with different controllers, so all may be used at different times.