Two of the pins (+5V and any GND) on the 40-pin connector can be used to supply power instead of going through the USB port. That's what I did with my beer-fridge controller: power for the whole system comes through the barrel connector on the 1-Wire/I2C interface board in the middle of the stack.
Guess I shoulda looked at the pinout before leaving that comment. What do you need for I2C? Is it more than some resistors? Hmm, I looked and it seems you just connect up the pins. Internal pullups? on-board? Leaves it to external? I am way too lazy to hunt through the docs to find out. Did you put in some fuses or something? My experience with I2C is so far limited to connecting Arduinos to IMUs and so on. Also did the SPI sdcard thing there with the sdfat lib. Hooray for electronic tinkertoys.