Hola Lufe.
Your CAN experience will surely be very useful. As I mentioned in my first CAN post, my humble role is to channel the efforts to let the CAN API be completed. So far, I must say, it has been more a behind-the-forum work between Arduino, Atmel and me. Tests are in progress; the CAN library is working using the IDE directly (no makefile) and we are close.
From all of this, we have learned a big lesson: DO NOT (I repeat) DO NOT try to build something from Atmel Studio ASF and introduce it into Arduino. Both software architectures are entirely different and it shall be a pain to remove unneeded references. This experience is helping us to understand better how to create a Due library. The updated libsam will be solid ground for future developments for Due. Saludos!