Hi smoothere hope you got it up and running now as I feel your pain. If not this is what I did.
Formatted both my sd card and usb stick
Download a fresh 3.2.1 retropie
Installed it and followed you tube vids techtipsta, floob and others f4 typing part where you over clock, explanded the sd card. Rebooted but still no nes or snes emu was dishearten. After I changed the usb stick to other ports (now mine in the top right one) and re explanded my sd card, in the retropie options (no typing.) another reboot and eureka happyness returned to me as they appeared and worked. I did no editing and haven’t change any of the emu all on default. I hope this helps you out and good luck.