I was thinking how the main board can communicate with the outside world. There's a debug serial port over which we could run PPP or SLIP, or we could use the ARM with its USB port to emulate a high-speed serial-over-usb link.
Secondly, i've been studying the schematics and I don't see any issues with plugging amiga mice into the joystick ports - the h/v pulse lines all go straight into the FPGA, and all three mouse buttons are accounted for.
However I think the ports will be only wired up to 3.3v according to the schematic.
Will this be a problem for autofire joysticks? Do they expect 5v for their electronics ?