There may be a slightly easier way to do this.
I've noticed that with custom packages you can override files that the the extracted files in the Data/Mods/ and Data/Public/ folder aren't able to, however you'll need to repackage your changes each time you change anything in those two folders.
The technique is the same as here:
http://www.larian.com/forums/ubbthreads.php?ubb=showflat&Number=508810#Post508810That is, create your Main mod override files, make a .pak from them, copy the .pak file to the Data directory of the game -- not My Documents\Larian\...\Mods! -- and it should theoretically work.