Rev. 3.2, firmware 3.2
Seems like it's finally perfect.
You can open FamicomDumper_board.dip and FamicomDumper_schematic.dch source files using DipTrace.
After assembling first write FamicomDumperBootloader.elf to STM32 uC, you can use J5 pads for it. Then program FamicomDumper.bin and FamicomDumper.svf using bootloader (see README.md).