Ok, new version. I just called it v1.1. Nice and simple.
The changes are pretty much what I mentioned before. Things in brackets are ignored. Instead of moving elements I just changed it back to four files to make it more manageable. I've also changed the "how to use" file but I'm not too sure about how easy it is to follow. I'm hoping that the program is intuitive so it won't be needed much.
Enjoy.
Edit: Looks like I broke bonus damage and maybe some other stuff but I won't release another version just yet since I think I've done that a few too many times. I'll just continue to build on my own copy until it seems stable enough and has all the features I may come up with and then release the next version after some proper testing.