@mitu Thank you and I'm sorry for not following what was clearly written down. In the future I will make sure I list all that is needed. In this case I figured out the solution but do appreciate the beginnings of the sites help.
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.
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.
@stoo Having lots of differences between FBNeo & MAME for system16 based hardware isn't surprising, system16 is a historical driver for Final Burn (first FB driver and first emulator to run that hardware, the emulator's name is actually based on "After Burner"), current FBNeo driver is built upon that initial driver. You should report the glitches at https://github.com/finalburnneo/FBNeo/issues, we can't fix what we don't know about :)
@n33k33 Please don't bump old topics, it's rude. @mediamogul hasn't been active in the forums for 1 year, so it's unlikely they're going to get a reply.
Perhaps opening a new topic and explaining your issue will get more replies.