I have submitted a PR to fix the building and flashing of the FX2 firmware. Using this patch I can successfully build and flash my FX2 dev board. I also added details to the README about how to build the firmware using the corrections in the patch.
The only issue is that the
hdmi2usb-mode-switch command requires root permissions to flash the firmware, thus using the Makefile means that everything is built as root. This needs fixing