I'd add I2C/SPI I/O expander to encode with resistor net version of the board and some unique ID chip.
Like it was done on EDA-03829 with MCP23017
Maybe DS18B20 or DS2401 for unique ID? It behaves reasonably good in radiation and is also used on FGCLite (TE/EPC).
Check #27 (closed) for hints how to get some more free FPGA pins.