Hello Ben. All above sounds great. I have a question. Have you been able to run the blink example in your board? If not, I can provide a test .bin file with a blink example for SAM3X8C using AS6. I just need a digital pin (PA or PB) where you can connect an LED or that has already a built-in LED connected for this blink test. At the end of the day this is really a "shot-in-the-dark" that could help you to save some R&D time.
-p