Number 1 should be pretty easy. In the PEQ PHP editor you just make a faction and set its base attitudes, then assign that faction to the appropriate NPC's.
Number 2 seems a bit more tricky. I've never added new item fields or spell effects, so I can't tell you how involved it would be or if it would even make any sense to the client, but that's probably what you'd have to do. Someone more experienced may know of a better way to do this.
Number 3 shouldn't be difficult at all. You could track this with a faction so that killing the good guys reduces your G/E faction and killing bad buys increases it. Then in your quests you just get the players value for that faction ID and adjust your dialogue accordingly. If certain responses should incur a faction hit, you can do that with the quest system as well. You could even set up your faction hits table so that relevant NPC's even become hostile. In fact, this really strikes me as what the faction system was designed for, it's just more granular than Good and Evil in game.
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