Amonchakad, there's another piece of software, this time coded in Python, that does similar things like this Perl script, concerning combining nation mods only(?) by pyg, in case you want to try it out:
http://forum.shrapnelgames.com/showthread.php?t=42530
http://forum.shrapnelgames.com/showthread.php?t=42415
It requires a bit of programming knowledge from the user to use it, but it's wonderful code and a very interesting concept to create multi-nation mods or games.