As I improve the board design in my head, I think I can eliminate the EEPROM and downgrade the ATmega to an ATtiny. The design will now read files off an SD card instead. The ATtiny will populate a bank of the SRAM and present that to the 6809 as ROM, using the CPLD as a stand-in for a series of ‘595s. The ‘tiny will also load the FPGA, both from files on the SD card. I’m assuming that Xilinx FPGAs can be loaded with SPI or something similarly pin-frugal. This feels like a better, more modern approach. Moreover, I wasn’t looking forward to reflashing the EEPROM throughout development.
Also, an amendment to my component count estimate: I forgot about power. So we need to add a few SOT-23 LDOs for the various voltages (1.8, 3.3, 5.0). But it’ll still be a very small board.