In the meantime, let me at least validate all of the other stuff I can before decabling *again*.
FPGA and MCU firmware seems to be at MVP level (that's "minimum viable prototype", as in all core functionality needed for operation has been demonstrated but not necessarily fully debugged).
In particular, I can plug the device into a 10/100/1000baseT LAN (the SFP+ side still needs more work but it's functional without that) and it comes up on a hard coded IP address because I haven't got around to adding UART console commands to change that. It's reachable via SSH using a hard coded username and password and gives you a shell equivalent to what you get from the UART.
There's a SCPI server on port 5025 that provides commands to change direction of bidirectional ports, set threshold of inputs, and set swing of outputs.