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.

Hello,

I have this same issue and after some research i have determined that it is a problem with how wminput uses the blue-tooth adapter.

Here is an old Ticket for wminput that explains the problem a little better.
http://abstrakraft.org/cwiid/ticket/71

Using -d appears to be what causes the issue.

When I remove the -d flag I can ssh into my raspberry pi however with -d enabled I cannot.

HOWEVER:

By removing -d you cannot add a wiimote after the system has started.

You can connect them when the retropie screen appears by pressing 1 and 2.

Yup no problem. I also feel like the guide should be more specific in stating the SSH and terminal spam problem, other than in the issues section that may not be noticed. I'm just not sure what section to state it in.