I have an update to this. You might have noticed that the .kl file gets wiped every time there is a system update if it is put in /system/usr/keylayout/. Since Ouya has had an update a week this is a problem. Here's the solution for that...
In the android dev site I found this information about the .kl files:
The major difference between /system and /data (not noted here) is that /system is what is wiped and replaced when the Android image is updated, so it is a bad spot to put user fixes. /data is where all your user settings and packages go and they are left untouched on an Ouya system upgrade.
So, to put it in a nutshell, but the Vendor_20a0_Product_0001.kl file in /data/system/devices/keylayout. You will probably need to create these directores on your Ouya. I did on mine and it works as this is a basic Android behavior for Android keylayout files.
I held off on posting this to make sure that I was correct. After the Ouya system upgrade from this week it still continues to work.