You can't rebuild everything. Some things like the elevators, etc. are hardcodet.
And, you don't need to "clean off" everything. You just need to make new maps, new scripts, etc. and a new exe file, that loads the new start map. (created with the loader creator or what so ever.)
Hi there! "Prosper" Here's what you can do for start:
1.use fo2 mapper to make new maps, place objects... design stuff
2.give your critters some scripts...
There's so much you can do once you start your own mod, whole fallout world is in your hands
Here's one very useful address to help you get started: http://modguide.nma-fallout.com/