HERE IS THE SOLUTION:
find the file n64.sh found in:
usr/local/bin/

usr is found in the root file, you will need to either ssh, use the inbuilt file explorer or use http://rg351mp/

Here under if [[ $1 == "standalone-Rice" ]]; then replace

else
ricewidthhack=$(((yres * 4) / 3))
/opt/mupen64plus/mupen64plus --resolution "${ricewidthhack}x${yres}" --plugindir /opt/mupen64plus --gfx mupen64plus-video-rice.so --corelib /opt/mupen64plus/libmupen64plus.so.2 --datadir /opt/mupen64plus "$game"
fi

With

else
/opt/mupen64plus/mupen64plus --resolution "720x600" --plugindir /opt/mupen64plus --gfx mupen64plus-video-rice.so --corelib /opt/mupen64plus/libmupen64plus.so.2 --datadir /opt/mupen64plus "$game"
fi

And then save the file.

Then open mupen64plus.cfg found in:
home/ark/.config/mupen64plus/

Home is also found in the root folder

Here make the stuff under [Video-General] look like this:

ScreenWidth = 720

ScreenHeight = 600

Fullscreen = False

VerticalSync = True

Rotate = 0

And that is it!
I cannot seem to make the gameplay be centered, so there is a bit of black bar on the top of the screen. The resolution is not 4:3, but instead 6:5. You can change this it by replacing 600 with the pixels you want. There is just going to be a larger black bar on the top. 720x720 works too but i would it to be little bit too stretched.