Seems that no matter what I try, upgrading the structure isn't free. 

Do you mean that it still charges you, or that upgrading isn't presented as an option? If the latter, I think this is because it only displays client side if the player has the resources in their inventory.

Ahh so you still need at least the amount of required resources to build one, and then it won't charge you?

Yeah, the plugin is server side so it can block the charge, but the client has to think it has the items or it won't display the option, or send the message to the the server when selected I assume. The Anti Items plugin attempts to solve this problem by placing the items in the inventory out of view in hidden slots, but the approach has some problems. I've been working on a hybrid approach that networks to the client that they have the items in a hidden slot, and uses server side hooks to block the charge. It solves some issues and also creates others. Still havent decided which plugin to add it to or what to call it since it works for crafting and other things as well.