So if I understand you have successfully flashed the boards, but are unable to get cgminer to recognize and begin mining with them?
I'm curious how did you actually interface with the boards to flash them? Is there a USB connection, or UART maybe? And once they are flashed how did you connect them to the Pi? I'm hoping its standard USB, but if its UART or something else that complicates things.
It is UART. There's a way to connect them easier to the pi with a UART USB adapter. I have not tried that, but the guide I linked shows you how to use those too.