Wow whats with these Bonnes and retaining water in places? My door moulding retains water after it rains. The car can be almost dried and when I open the door, I get a small waterfall. Same for the rear trunk area where the lip of the lid comes down. That little plastic runner piece? Holds water.
As far as my windshield, It was replaced new not too long before I bought the car, so no pitted glass
What you can probably do is bring it down to bare metal, and see if there are any little holes from the rust. If there is, you might want to skim coat it with Bondo then sand smooth, prime and paint.