Re: Challenges -- Sounds like a good title for a future blog post: "The Toughest Challenge of OpenPCR". Off the top of my head, 2 challenging areas were the mechanical design of the heated lid and super-hacking Arduino for our USB control. For instance with the heated lid, we knew we had to have a flat hot surface come down on top of the PCR tubes. We went through several mechanical prototypes, and learned that the high tolerance of the heated lid meant that the tolerance for the rest of the device needed to match. Not giving you enough details at this point, but look out for that "challenges" blog post in the future :)
Tito