so when you put the stock deck back in it did the same thing as the kenwood? Or it worked fine?

Usually, if ONE speaker has a short, it will send the amp into a protect mode, so NO channels will work. its possible that when you were changing decks and tugging on the OEM harness, that a wire chaffed on some metal and now you're getting a short. Check the OEM harness that is comming out of the dash... look for any abrasions or bare wires.