I took out the second set of cats in mine. There were no problems with a mil lamp or anything. I can't speak for emissions though. One performance exhaust company says the second set of cats is purely for sound reduction. I don't remember what brand, but google performance exhaust and it's not hard to find. Perhaps they can answer emissions questions.
P.S the machine sounds awesome now, in cab growl is perfect with no droning while cruising. I inquired about a different muffler and the muffler guy said the stocker is not restrictive enough to worry about changing. He also said that any other muffler will be incredibly loud and wont fit properly. replacement systems are usually way thicker, meaning they will hang down and look goofy, in addition they will have a huge gap between them. If you are wondering, the power increase was noticeable with the cat removal.
