Thanks so much for your reply. It gave me the confidence to persevere.
I eventually found an error on my PCB design which left pin 57 floating, rather than connecting it to +3.3V via a 10k resistor.
After correcting the issue, the STM32 appeared in the Netduino Update Tool as a device in DFU mode. I was able to flash it with the Netduino firmware and then load my own .NET code onto it through Visual Studio.
So I've confirmed that it's possible to create your own custom Netduino 2 PCB using the resources available on the Netduino website (schematic, firmware update tool, etc.).
Chris, thanks again for your support!