http://www.xbmchub.com/forums/threads/9749-HOW-TO-GET-ANY-REMOTE-CONTROL-TO-FULLY-WORK-WiTH-YOUR-OUYA
Ok. Here's a little walkthrough I found on editing the button info for the OUYA
What I think you'll have to do here is open the text file that the OP talks about and either add in your button that you want from your remote to open the Home Menu, or replace the Y button with it. As far as what code the OUYA will read that button as.... I think that's what KeyTest is for.
So, you'll have to bind the button you want, to the key you want "F3 you said works on your keyboard but does nothing on the Flirc, so use that), then press the button on the remote with KeyTest open.
Sorry, it's such a pain, but this is the best I can find on it.
Someone on there said this video helped them out as well.