I'm just going by my memory now because it was summer 2007 when I did it. I have never thought of checking it since.

I cleaned the area, brushed a rust preventor on and let it dry; I then put a thin layer of clear silicone over the welded track sealing where the rail is welded to the door, and then let that dry. I then put the rubber back into the track using a popsicle stick and my fingers.
I then popped the two plugs at either end of the door and sprayed as much WD40 inside the doors and along the bottom of the door where the rubber/track is. Spraying inside the door was done just in case the moisture was leaking from inside the door but sounds like that really is not the case.

I will try to remember to recheck both doors when the car comes out of storage this spring.