Hi Matt,
I can think of two options for you to try:
1. Edit your retroarch-core-options.cfg file in /opt/retropie/configs/all and delete the mupen64 tags at the bottom. This should *hopefully* get rid of any bad settings you choose, and regenerate some defaults when you reload the emulator.
See here if you need some help with this, or copy mine (use the “rice” gfx plugin option though!): https://www.youtube.com/watch?v=lh0n5PWN2lI&t=658
2. Is dependent on if you are using a second config file in /opt/retropie/configs/n64. If you have a retroarch.cfg file in here, delete it using rm *filename*.
Let me know how you go!