Over the course of a couple evenings, I got every part of the system working... except USB.

That means the card I/O system works, the user interface (which is to say, the lights and button) functions properly and the encryption system interoperates with the previous versions correctly. I've even managed to perform a simple preliminary performance test which seems to show that it's able to read at a rate of something around 1 MB/sec - not quite 10 times faster than the previous version.

USB is the current sticking point. The USB interface remains completely and totally inert. I suspect that the hardware functions properly, because if I short the erase jumper, SAM-BA brings up a CDC device that works properly.