I am writing this suggestion from the very heart since I literally wasted a complete 24 hours cycle trying to reinvent the wheel. It would be GREAT (!!!!) if you guys could make a folder with scripts for configuring the MUXes. The folder should be part of the standard distribution. In fact I think this would ease the adoption of the board as a whole for newbies.
I always knew there was a Hardware guide but I didn't care going to section 11.6 (i2c in my case) until after many frustrating hours of misunderstanding the tables on the earlier pages. I can imagine how relieved I would've been if there was a script (in e.g. /local/scripts/) which I could simply execute to change the MUXes to output I2C on the pinouts. We could save many more engineers from wasting time figuring out these things.