Excuse my French, "Certains chats croient qu'ils sont des chiens.", but what the hell are you doing this for??? I dont think you can really make a list of all the scripts. Theres can be an infinite number of scripts to do an incredibly large number of things. If you need help with a script, just ask us and we can help you write it, or tell you if its needed. I do not recommend cleaning everything as you say you are, but it depends on what your doing with it.
I'm working on a Total Conversion. We have no need for a lot of the Vanilla stuff. We're trying to clear out the backend so it's a little cleaner and easier to manage. I've been running through this with Yossarian22, creator of the GTS mod, as he's already done some work in this area (he is using the German version though so I have to start from scratch) Basically, we're wanting to create a modders resource with a blank version of the .esm that only contains resources and none of the quests, dialogue, scripts, NPC's, areas etc that you wouldn't need if you were doing a big TC project or something similar.
As for the scripts, there aren't infinite number of scripts, I just want to know the functionality and necessity of vanilla FO3 scripts to see which ones are necessary to keep. IE I don't need the scripts CG01* - CG04* because we aren't using the original start, but I do need CG00 (in a modified state) because that handles the game starting and fudges things up if it is removed.
Was just curious if there was a list of vanilla scripts, what they did and if they were necessary so we wouldn't have to duplicate work if there was.