@stattmone If you're using the standalone emulator, then the configuration you've done have no effect. Look in the /opt/retropie/configs/n64/mupen64plus.cfg file and re-arrange the controllers there (look for [Input-SDL-Control1], [Input-SDL-Control2], etc.). The same file is available at \\retropie\configs\n64, if you're using file shares to access your Pi.
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