I'm not thinking it'* the sunroof drains only because when mine were clogged my headliner got wet. You can easily check them like I did with a jug of water. Just park it at an angle and open the sunroof then pure the water in the channel so it can drain down the tubes. Then you'll know if there clogged. My front two (all of them are in the corners) wouldn't drain. I blow air in them to clear them.
I would suspect the Butyl in the door that may have came loose and is allowing water to come in like my rear drivers door just did, not sure how this relates to your other problems though.
I removed the lower trim along the rocker panel and sat in the car with the doors shut as my wife flooded the car doors. After a minute I could see water coming in. I pulled the door panel and found the seal loose. I went to Advance Auto and bought a roll of Ribbon Seal for 8$ and replaced all of it in the panel. No more leak.
Hope this helps. Look at the links in post #1 and #3 http://www.bonnevilleclub.com/forum/...ic.php?t=88557