Ok, cool
It helps because OoT3D is a functional Homebrew exploit, and because of how Powersave encryption works, Homebrew would be your only way to inject a working save file into your Pokemon Y
https://github.com/yellows8/oot3dhax/releases -Grab the latest release (top)
https://github.com/yellows8/oot3dhax -Scroll down a bit and follow the guide typed out
After you install OoTHax (It won't hurt your system, and yes you can uninstall it later) follow this guide
http://pocketmonsters.shivtr.com/forum_threads/2005976
After you go through both guides I'll give you a few more instructions