Are you wanting to edit and / or remove files just from the OM (or some other) mod? Or will you be wanting to remove parts of the Stock game?
The easiest way to make your own campaign, is to take what is in the game and edit that. If you're going to be wanting something closer to OM than Stock, then use the OM mod as your base. You would use the Mission Editor for the graphical help it can give you, and then a text editor to clean-up the files if necessary. If what you do is for your own personal use, no permission from another mod's author is necessary. If you want to change things and then release what you did as a mod for others to use, then you should get permission from the original author.
A potentially useful, but very "dangerous" tool (for your game install) is available in the
JSGME applet. Follow the link in Mike's post for the
JSGME v2.6 User Guide PDF and read on Page 17 the "Notes For Modders" section. I'll warn you right now, you have to be very careful with that. It is not to be used lightly or off-handedly. There is no warning in the manual about the possible hazards of using the directive. The FotRSU team is now so wary of it that we are refraining from using it at all, if it can be avoided. You cannot use it if the file is being replaced by another, else the original is deleted, never to be recovered, which is NOT cool to do to someone else's game... you have been warned.
I just went looking, and the site for the [ENG]Mission Editor V17.pdf is no longer available. If you want a copy of that, let me know, and I'll send you one.