Since only js0 and js1 exist in the input directory, I assume that only SNESDev is running and not interfering with, say, the gamecondriver (which can also be installed via the RetroPie-Setup Script – DON’T DO THAT!).
Also, one pad is working, which means that all connections except one data pin are properly connected and SNESDev is running correctly.
Now, I would try and check or even reconnect the data lines on the breadboard. Just a wild guess, though.
I keep my fingers crossed that you can solve the problem until sunday!