EDIT: I tried both lr-fba and pifba and none of them worked. Am I simply using the wrong emulator?
What do you mean exactly? If you’ve got a romset of a certain version (for instance 0.154 for the lr-fba) then you can read here how to use the various FBA versions (lr-fba, pi-fba, etc.) w/ those ROMs.
I, unfortunately, do not know how to use clrMame to convert one romset version into another. I own romsets from long, long ago that work w/ Retropie’s Mame and GnGeo-Pi. Also make sure you’ve got a working BIOS file for the Neo Geo and that it is placed in the proper place (i.e. for GnGeo-Pi in /home/pi/RetroPie/roms/neogeo).