Where does your exhaust end? Does it go all the way out back beyond the bumper or rear valance, or does it end in front of the rear axle? A buddy has the same problem with his AAR with the stock side exit exhaust. When he is stopped and at idle, the fumes come up thru the side glass when the windows are down.
OOPS I just noticed you said the fumes under the hood were really bad when you were working on it.
The change to the bigger cam may have you running a lot richer than before. Have you checked the plugs to see if it is too rich.