Thank you both for your help, I visited the customer last week with a replacement Duex5 in hand and the issue is now resolved.
It was the board and not the ribbon cable, as I exchanged the cable first and the issue persisted. But upon swapping out the board as well, all function was restored and the machine completed a test print.
Two notes to close this up, I would recommend having a way for the expansion board to report these Short to Ground issues using the driver numbers included on the board (5-9) rather than the local numbers, because that was a contributing factor to me running down the rabbit hole on the mainboard rather than the Duex.
Second, we need to have a conversation about who is liable for the replacement board because I believe the machine has an extended warranty that is still active directly from Modix. I have the defective board and it's ribbon cable at my desk and can ship them back to you if you would like. Let me know what the best next steps are and I'll be standing by to finish this up.
Thanks again,