I had a similar problem just now. I’m backing up my roms folders (don’t want to have to re-run es-scraper! Had to do the same PIL/Image text line change that you did).
In my case, I couldn’t find ES-input.cfg either. I had to run this from commandline:
Emulationstation will run you through the initial controller setup the next time you run it.
But weirdly, after doing this I no longer see all menus in emulationstation. It cycles NES -> SNES -> RetroArch Input config, and then it just stays on that “Input” screen. Been playing with my install a lot, now I know what I want, so I’m just reinstalling anyway.