one way i thought i could do this is by using ammo script to place a item in the targets inventory, then have a quest that tracks that object. The problem with this is i don't know of any items that can be tracked by quest.
the other way is to use ammo script to attatch a marker to an actor when you shoot them and have the quest track the marker. the problem with this method is i don't know of any script commands that would make a marker "stick" to an actor/NPC.