For the ones with a number I get an error like this
Thats OK, the Main.pak and Textures.pak are multi-part packages, you only need to extract the main file (Main.pak), the other parts (Main_1, Main_2, ...) are extracted automatically with it.
Assuming the game loads the scripts dynamically as needed we can likely change EVERYTHING we want, assuming we can get the game load loose files, or maybe the unpacker can "pak" and we just number them main_2.pak and it loads that ?
It seems that the engine prioritizes unpacked files over packed ones, thats why creating a Main folder inside Mods prevents the main campaign from working for example, because in that case the engine assumes that everything for the module Main is in Mods/Main/, even though its an empty folder. But adding some kind of hook may be possible.