I'm not 100% sure on what you're trying to accomplish, but it sounds like you used the "item selection" section on custom abilities, when what you want is the "Allow User Text?" box to be checked under the next section down.
As for replacing abilities on archetypes, can you be a little more specific on what you want? Do you mean you want to replace Cass Specials or do you want to use a different list of Custom Abilities?
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