Time to take a break and stretch for a bit. This is excellent progress.
All of the functionality needed for a minimum viable system now appears to be operational other than the trigger inputs (not tested yet, but I see no cause for concern at this point).
1000baseT is more than enough for SCPI remote control of stuff plus SSH debug console, plus letting me build out a whole bunch of functionality in my general embedded instrument firmware stack.
The GTXes were really just included on this board as "the FPGA has them and I feel bad not hooking them up to connectors".
That, and I'm low on baseT drops to this bench so running the board off a fiber drop would be convenient. And a CDR trigger would be a nice stretch goal to have eventually.