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When creating a custom ability, the second option is "Secondary Custom Ability", check that to make the ability show up in the secondary list, instead of the primary.
It sounds like you're going to need to store the initiator level somewhere, so that you can modify it.
My first thought on the subject would be to create a new item on the Special tab - leave the "Show in Specials List" option unchecked, because you want this to be hidden in the background, and at the top, make it unique. Then bootstrap it from the classes that need to know how many initiator levels they have.
Then, you can have all the classes that grant initiator levels add their number of levels to the field[Value].value of the special, then when you're deciding what powers are available, look up the Value field on that special.
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