I haven't done any modding to the main campaign myself, so I don't really know an awful lot about the process. With that said, I'm just going to point you in the direction of Rhidian's work on this:

http://www.larian.com/forums/ubbthreads.php?ubb=showflat&Number=529996#Post529996

I think that your modification needs to follow the steps contained in the first two spoiler boxes in that thread's opening post (the first spoiler box for how to apply changes to an existing save, the second spoiler box for how to apply the modification without the 'corrupt main.pak' error).

Hopefully someone'll come in and correct me if I've got this wrong. smile

Escape From Smalcatraz: Steam/Nexus. Forum thread.