HI ajw, I suggest you start fresh and download the RetroPie image for Rpi2 from the downloads section on this site.
I use the Pi2 over clock setting and find that is all I need, also set your gpu mem to 128meg.
I see you have seen my other comparison vids, but did you see my n64 setup vid? That can help you setting up mupen with the rice plugin which I find works best, good luck!