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I realised that I'd need some extra hardware to connect the PCIe card to the console panel. The I/O pins on the Xilinx board operate at either 2.8 or 3.3 volts, and my console panel circuitry operates at 5 volts. So, what I need is some level shifters. I got four of these 4-way level shifters, and put them on a piece of veroboard with connectors for the Xilinx board and a 50-pin ribbon cable.
The 50-pin ribbon cable terminates in an HD50 connector (commonly used for narrow SCSI applications) on a PCI bracket. The panel has been fitted with the same connector, so a SCSI cable can be used as an interconnect between the PC and the panel.