I think we need to figure out how SDL sees the touchscreen because this section of the config file:

# Mupen64Plus SDL Input Plugin config parameter version number. Please don't change this version number.
version = 2
# Controller configuration mode: 0=Fully Manual, 1=Auto with named SDL Device, 2=Fully automatic
mode = 2
# Specifies which joystick is bound to this controller: -1=No joystick, 0 or more= SDL Joystick number
device = -1
# SDL joystick name (or Keyboard)
name = "Keyboard"