I know the item is ingame, but both the CS and TES4Edit are saying there are no users, nor are there any references to the item. I'm pretty sure the NPC wielding the item doesn't spawn until the player reaches level 20 or so. However, shouldn't there still be a Users #, even if the User has not spawned yet? I'm really hoping that I'm wrong, since otherwise I'll have to mess with the leveled lists to properly add the item

Whether you added the item directly to the NPC or via a script, it will still have a user count of 1, because either the NPC or the script will then be using the object. Occasionally the reference count and users count doesn't update until you save and reload the plugin, no idea why this happens.

This item is in a Leveled List? If my memory serves, the Count gives you the hand-placed items (direct, not via leveled list) and the Uses gives the number of direct references to the item in scripts etc. so both would be zero if ONLY leveled list entries refer to the item.