One comment: Your report says that the problem with the 5V
resistors cannot be remedied. This is not so. The
the 5V pullup  resistors on the DIO can be disabled by removing the
Jumpers: JA1, JA2, JB1, JB2, JC1, JC2, On the DIO card (Adlink PCI-7248).
Removing this jumper will render these lines passive.

The Documentation for th card is located here.

A coarse layout of the card is on p9. A description of the jumpers is on
p17.  The labels on the layout are impossible to read in the pdf version.
The layout shows the Connectors, the eight jumpers present on the card and
the PCI controller chip.
The jumpers I am referring to are the six located closest to the top of
the card.  Paolo may not even need to remove the card to pull these.

If you want to fix this problem I suggest two things:
1.) removing these jumpers.
2.) Installing pullup resistors in the Mirror heater chassie, which
has a good 5V supply when the heater is off.