@kiphouse checking the Mupen64 documentation: http://mupen64plus.org/wiki/index.php?title=Mupen64Plus_Plugin_Parameters I think you should be able to do this, try:

X Axis= button(0,1)
Y Axis= button(2,3)

You will need to get your button numbers. In the settings above, button 0 is left, 1 right, 2 up and 3 down.