Definitely go back to the stock induction system. As for the aftermarket cat, as long as it does it's job it won't matter. If they ask about the cat, which they won't because they don't put the car on a lift or anything, tell them you hit a rock and it mangled the stock one. It is illegal to change the cat unless it is a certain age or it was damaged. Just make sure your stock induction system is back on or it will fail visual automatically. Good luck, mine's in February.
