Several years ago I did a major fix on my sunroof. The problem is the window frame has a cupped "U" channel around the edge that collects water, salt etc., very bad design.

I pulled the glass and frame out and bought a new factory seal. I then attacked the rust with wire brush and sandpaper and used one of those rust-turned-to-primer treatments and painted with rust paint. Used silicone seal to attach the seal and reinstalled.

The drains can be flushed with water from the bottom, or air or a probe. Here we get Mud-dauber wasps which build clay homes in the drains.