If you create a custom board, you may need to recompile the firmware (tweaking to match your board's crystal frequency, etc.) Check out CW2's Netduino 2 Firmware v4.3.1 with GCC support thread for tips on how to get started.
Can you provide all the files needed to load a custom board with Netduino firmware / bootloader. When I load this DFU in the STM32F405 and reset the board, I cannot access the device through MFDeploy. Is there another file I need to load?...tinybooter, tinyclr, or something?
Once you build the firmware, you'll end up with TinyBooter, TinyCLR (ER_FLASH) and a configuration sector. You can use STDFU tools (or a C++ IDE like Keil) to load those onto your custom board.