Utmikeg - yes, I was referring to the optional roof lights. These came standard on our 3500 series. Our windshield was not touched during the repair.
If it helps, our whistling noise was identical to the sound recorded on the video that a previous poster attached in this thread. If your noise sounds different, then the solution may be something else (i.e. windshield molding, on star antennae, mirror?) Good luck and I'll post here again if the noise returns.