Hey guys! I'm new here and I must say that this article helped me a lot. I managed to get my OUYA working with FLIRC, XBMC and an Apple Remote.
In case anyone else wants to accomplish this, I created a guide (in English) on how to do so. I modified the files you provided above in order to have full functionality.
Cheers for the great work you guys do!
Here's my tutorial:
http://www.peterfranssen.de/2013/08/04/getting-flirc-to-work-with-ouya-and-xbmc/