Thanks all, we finally got this working correctly!
We can now make both custom skills and custom items that use those skills, and have them link up correctly on the character sheet. The key was knowing that you have to drag-and-drop both skills and items, and edit those copies.
That said, I'm not sure how we were supposed to know how to do this? The drag-and-drop mechanism is not exactly intuitive, and there isn't anything obvious saying that you need to do that to get this stuff working. It sounds like a lot of you just know this from the MgT1 ruleset... but there doesn't seem to be any documentation for the MgT2 ruleset... so that's why I've been asking so many questions (and was so frustrated).
It seems to me that for the price we paid, there SHOULD be some kind of documentation... even if its just a copy that comes with the MgT1 ruleset. Or, maybe we should have a sticky post at the top of this forum, where the developer and users can document these kinds of tricks. I think it would be good to make it so the next newbie doesn't have to go through what we did.
Anyway, thanks again for the assist. All's well that ends well.