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You need the new ECU and two pre-programmed uncut keys. Then get just get the keys cut to match your old ones and thats it. Dealer not involved.
A junkyard ECU wont work unless you find the keys with the truck, or have the ability to program the ecu (forscan can do this) the dealer probably won't touch it. A good locksmith might.
The other parts involved in the PATS system are not vehicle, key, or ecu specific. Only the keys and ecu are a matched set.
Im curious how exactly the mechanic started your truck with another ecu...