I would make sure that both the class helper and the class levels are replaced in the user file. Maybe you only put the unique ID for the class levels in the Replaces Thing field, and didn't do the same for your class helper.
By the way, a good way of looking up how to do things is to pattern your own code after what has already been done. There is a large body of d20 stuff entered by myself and others whose examples might or might not help. You sound like someone who already understands coding, much better than I do, but I have managed to make things in the editor seemed daunting at first.
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