While I am changing the SPI routing, Jakub has convinced me to replace the AVR with the ARM7S chip he uses for the hardfile demo. Amazingly, the cost of the chip and the USB socket is the same as the AVR. I have managed to fit all on the PCB, just need to fix the routing (again).
The main benefit is I can pick up Jakub's work for hardfile support, which save time. It also goes faster, and we have gained a USB port for flashing the microcontroller - and we can potentially use the USB port from the FPGA.
Updated schematics and layout in a few days. Assembly pushed back two weeks.
/Mike