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Turns out the problem was a short in the wire thats goes to that COP. The bundles of wires that sit behind the supercharger was sitting on top of the part of the ERG valve that comes up from the exhaust. The black corrigated plastic had worn off and the wire was touching the metal of the tube. Thanks for all the help!!
"The COPs will overheat if they are dumping their full charge at each firing event because of bad boots or a short at the secondary output--or if the primary is being continuously powered because of a short to ground on the negative side (the pink/white wire on #2) of the COP primary winding."