So what you effectively want is a system that will
- Autocraft blank patterns for AE (trivial)
- Input them into a pattern encoder (trivial, but remember it needs to do it a stack at a time)
- Take recipes from NEI and the corresponding items from your storage (I have no idea how this would be done)
- Encode the recipe (I think this is doable)
- Remove the pattern and input it into your MAC? (Simples)
As for crafting once you have the recipes set up, you could have a huge bank of chests with export buses and level emitters, give a redstone signal once to activate the "always craft" bus when your stock of an item falls below a certain level. Oh and an import bus on the other side of the chest.
Problem is you would basically need one setup like that for every item (or at least one for every 8 items if you use a better export bus).
Combine this with automated quarring and ore processing, and a system I dreamed up to autodetect low storage space, craft a new storage cell and input it into a drive and you have a sentient ME network, self-aware, conscious of its surroundings and capable of learning.
Fear Colin, for Colin is mighty.
) thoughts. Try and come up with something, preferably not using Turtles/Drones or the like, as an extra challenge 
