So I was able to make this work by simply unplugging the mouse from the pi, leaving the controller settings in retroarch for fceumm set to auto NOT zapper, and then under settings change zapper mode to mouse.
My wminputA file is as follows:
#IR for mouse REL - fps style
#Plugin.ir_fps.X = REL_X
#Plugin.ir_fps.Y = REL_Y
#ir_ptr
Plugin.ir_ptr.X = ~ABS_X
Plugin.ir_ptr.Y = ~ABS_Y
#custom buttons
Wiimote.A = BTN_RIGHT
Wiimote.B = BTN_LEFT
Wiimote.Up = KEY_UP
Wiimote.Down = KEY_DOWN
Wiimote.Left = KEY_LEFT
Wiimote.Right = KEY_RIGHT
Wiimote.Minus = KEY_ESC
Wiimote.Plus = KEY_ENTER
Wiimote.Home = KEY_LEFTALT
Wiimote.1 = KEY_LEFTCTRL
Wiimote.2 = KEY_SPACE
Nunchuk.C = KEY_C
Nunchuk.Z = KEY_Z
#plugin for nunchuk stick
Plugin.nunchuk_kb.Up = KEY_W
Plugin.nunchuk_kb.Down = KEY_S
Plugin.nunchuk_kb.Left = KEY_A
Plugin.nunchuk_kb.Right = KEY_D
Plugin.led.Led1 = 1
#EOF
#IR for mouse REL - fps style
#Plugin.ir_fps.X = REL_X
#Plugin.ir_fps.Y = REL_Y
works as a mouse in zapper games BUT not even close to as well as
#ir_ptr
Plugin.ir_ptr.X = ~ABS_X
Plugin.ir_ptr.Y = ~ABS_Y
so I'd use the ir_prt not ir_fps mapping.
I've found that if you forget to unplug your mouse before you start the game you can simply unplug it and the wiimote will take over immediately as the mouse.
If using a wireless mouse you must unplug the dongle not just turn the power off to the mouse. This could be problematic for wireless keyboard/mouse combos as you have to unplug the dongle and lose both keyboard and ouse function.
So far I havent been able to get the hot keys to work in game (even thought they work fine in emulationstation) to exit the game and have to use the keyboard for that unless you have a gamepad installed (which doesnt interfere with the wiimote as a mouse as a zapper) then you can use the game pad to exit the game.
