Personally, I would keep it as Master Craft per the rules. However, I also would add in special formulae and ingrediants. An example would be for arrows of flameburst to require that the arrowheads be made of the teath of a fire-based creature. This would thus require a skill more associated with ivory than steel or wood (Craft: Ivory Carving?).
Another thing I require is that the spells associated to the crafting must also be memorized during the process and then the energy discharged into the item once per day of crafting (discharge is similar to casting, although there is no effect, no component cost, no experience cost, etc). However, I also use Casting Fatigue rules, so this feature might be considered redundant without that effect.
I'm as yet undecided on a few things (as stated, I'm still working on the system), and there's a lot to work out. Also, such things are set for a specific setting (Aedon) and may be overly exacting in another setting (definately inappropriate for Oerth and Toril, for instance).