A mod Im using leaves the modded item in a barrel in a shop in Balmora. Taking the item gets me arrested though. Can I make the barrel neutral using the CS? The barrel is also added by the mod.

If you're just looking to get it out of the barrel, I think you could just do "player->setinvisibility 1" in the console and then take it. Are you sure the object isn't sold by the vendor?

I would imagine setting the barrel to owned by player or player faction would do the trick.

How can I do that? I'm looking at the barrel right now in CS.

I could just as easily add the item to myself via console, but I prefer to fix it at the root

In the extra data, just remove the current owner (scroll to the top of the list and there should be a blank selection).