I hate to ask questions like this when there are so many other questions like it, but none of the tips given on other threads seem to work.
As far as I can tell, controller input is dictated by three files.
The thing is, I'm not really sure what each file does. I know that es_input.cfg is supposed to be responsible for the initial controller setup the first time you boot up the OS. So I deleted it in order to go through the setup process again (of course, I did NOT make a backup of the file). The configuration process started up again, but now none of the games have sound and the controller only works on the menus. I have to use the keyboard to play games.
I have already tried running retroarch-joyconfig, but after following the prompts, it does not appear to have any effect. If I have to reset the OS from scratch, I will. Setting up the controller is proving to be a chore.