So when its raining, and the wipers are used, the door ajar sound and the dome lights come on for a second.. This happens every time the wipers move, either manually turned on or if the wiper delay is set. Any idea where to start to try and find this short? The plugs under the wiper cowl are all clean and the rubber removed, and no water getting in on the passenger side kick panel.

 

I was about to suggest that the smart junction box might have suffered water contamination. Although there's no water getting in from the cowl or from the cowl cover retaining grommets under the windshield, you might have rain water entering from the front right wheel well if the seam sealer behind the plastic guard is broken.