SOLVED! (at least in my setup)
Turns out the new beta version of the MAMEWAH front end, which I use on my cabinet, allows you to specify a completely different emulator on a per-list (lightgun list, for example) or even per-game (Baby Boomer (U).zip) basis.
So what I did was make another folder called 'fce ultra lightgun', like this:
c:/games/emulators/fce ultra/
c:/games/emulators/fce ultra lightgun/
Then I copied all the files from my original FCE Ultra folder into the new one, effectively creating two copies of FCE Ultra. I then configured each one separately:
Lightgun Version:
Port 1: Gamepad
Port 2: Zapper
Famicom Port: <none>
Non-Lightgun Version:
Port 1: Gamepad
Port 2: Gamepad
Famicom Port: <none>
Then, using the new beta version of MAMEWAH (1.61b1 --available only on the MAMEWAH bulletin board, not on the MAMEWAH site yet -- to get to the BBS, go to
http://www.mameworld.net and click on the Arcade OS BBS link), I set up my .ini files as follows:
FCE Ultra.ini
emulator_commandline c:\games\emulators\FCE Ultra\fceu.exe {8.3[rompath]\[name].[romext]}{nosafelaunch}
FCE Ultra/Baby Boomer (U).ini
emulator_commandline c\games\emulators\FCE Ultra lightgun\fceu.exe {8.3[rompath]\[name].[romext]}{nosafelaunch}
This way, when Baby Boomer is played (from ANY game list), it launches using the lightgun-configured version of FCE Ultra; all other games are played using the standard-configured version.
Works like a charm. Whoopee!