qgears should run in windowed mode all by it self, not sure maybe I changed it to respect the ogre config window, you could try to reverse your changes delete the ogre.cfg (maybe qgears.cfg) to get the config window again and just disable fullscreen in the ogre config dialog
as for what todo
only thing that comes to my mind would be to try and run qgears on some of the original ff7 files, check out the unit tests maybe, I left the resource paths etc in the code and I'll try to be available on irc, I'm on gmt+2 though
maybe we should try and get a ticketing system
source forge most likely has one the project owner would just need to enable it
the command line switches should actually work, I use the program-options package from boost for that, so maybe just the right version is needed, maybe you could come up with a unit-test for them?