I followed your guide and the keymappings are working perfect with my media center remote, thank you!
I tried this solution to prevent having to re-root and replace the keymapping file.. it didn't work. My OUYA button mappings wouldn't work until I placed Vendor_20a0_Product_0001.kl into /system/usr/keylayout.
The issue I am having now is after ~5-10 minutes the OUYA says there is no controller present. I can use my media center remote to get rid of the message but then it shows up a few seconds later. The only solution for me now is to periodically turn the OUYA controller back on.