1) Figuring out how to work within the very low (but reasonable) amount of RAM each core has. They're independent computers, so each core needs to store its code and its data, all within 64 18-bit bytewords, which roughly corresponds to a tweet of information if you tweeted in UTF-8.
2) Dealing with the IDE: the IDE is attacking a problem nobody's solved: parallel compilation. That being said, it has been the second greatest challenge so far, after
3) Getting the hardware set up. My co-project-doer is light-years ahead of me in the EE department and makes most of the EE decisions, with some input from me about what capabilities the chip needs to have (a minimum amount of off-die RAM, say). Sourcing parts is something I would not have been able to do on my own, so I'd say this project requires a good deal of electronic literacy, if not dexterity.
That being said, though it's a bit of a prima-donna, it has every right and reason to be. It's an amazing, amazing chip. It's fast, powerful, unclocked, can work with all kinds of devices, is a crazy bargain both in hardware cost and in energy cost, and best of all, for me at least, an endless source of fun, hard problems. It's a fascinating chip.