Alright quick update.

I went back through the SNESDev github page. https://github.com/petrockblog/SNESDev-RPi#snesdev-rpi

I was able to get my first controller to be recognized and it seems to be working correctly but I had to use putty to ssh in and run sudo SNESDev. If I close putty it stops working.

On the github page it says to run:
sudo ~/SNESDev-RPi/bin/SNESDev &

This fails. I am am not sure what is going on.

I also tried to run:
Running SNESDev as a service

SNESDev-RPi comes with a script that allows SNESDev to be run as a service. The installation command for that is

sudo make installservice

and that fails. I think I am close but I am still missing something here. Can someone who has set this up chime in?