Which errors do you have exactly, and when do they occur? (in story mode, in GM mode, ...) Also, you should put story-specific scripts under the DOS2ModWrapper, and GM-specific scripts (if you have any, which is very unlikely) under GMModWrapper.
Story only uses the files you added/overrode. You can see those in Mods/YourMoreName/Story/Goals/RawFiles. You can remove any story files that you accidentally override from there and rebuild your story to get back to a clean slate as far as story is concerned.