What you're trying to do acheive with your mod is pretty complex stuff, so if you're wondering what to do next I'd suggest backing-up what you've done so far and creating a new gamedata folder for the purpose of practicing some stuff. Then maybe set yourself a few tests, for example adding a new mission to one of the npc's in the rookie camp that spawns some mutants you have to kill with some items as a reward, creating a new weapon or armour, messing with all.spawn etc. This way you'll be learning how everything works without getting bogged-down with having to make it work together within the game. Then when you come to actually working on your mod you'll have a much better idea of what you need to do and how to go about it, and you might have some bits and pieces you can transfer across fairly easily.
Like I said, I'm not experienced with modding, so I can't help you much in that respect, but patience and perseverance is the key, all the best modders started out with the basic stuff and worked their way up.
Anyways, good luck with it, I'm looking forward to seeing how it turns out, might give me a reason to revive my copy of shoc
Instead of the long and tricky job of extracting the AI from the mod, I can give you a link to 
