Another note, at some point when disconnecting and reconnecting my N64 controller, the custom settings I set were overwritten. Not sure why this happened, I do not want these settings overwritten.
Is there a way to set the InputAutoCfg.ini file for n64 to read only so that only I may edit it?
In the meantime, I redid my process, and made a backup copy of my file, so if it happens again I can easily replace the file with my settings.