HI trimmtrabb.
I did a fresh install yesterday and managed to get the pad to work using the following script and entering the controller keys.
sudo chown pi /opt/retropie/configs/all/retroarch.cfg
cd /opt/retropie/emulators/RetroArch/installdir/bin
sudo ./retroarch-joyconfig -j 0 >> /opt/retropie/configs/all/retroarch.cfg
I then got in to the retroarch.cfg file and copied it to the same as your file. Now the buttons are all over the place.
Any ideas?