Hi Jim
I just had the same problem with a post coupe. I removed the window/ track and took a good look at what had rotted and repaired it for less than $10.00
The part that rotted out was part of the U channel that holds the long rubber strip. It rotted out where the factory spotwelds are.. I cleaned the channel then measured the leangth and width then went to my local hardware store and purchased a quarter inch wide by 36 inch steel strip ( less than $10 ) cut the steel strip the leangth of the channel..and put it on the side for use later... Now take the upper window roller track and drill out the 2 spotwelds using a 1/8 drill bit (these are your factory allignment holes) Take the U channel turn it over and place the new strip over it mark the spot of the factory welds as close as you can and scribe a line and drill a hole in the center. Now comes the fun part !! Mig weld the steel strip to the U channel, then pop rivit the U channel to the upper window track using the 2 holes (the rivets are used to hold everything together until it is welded ) then mig weld the upper window track to the U channel..
when it all cools down drill out the rivits, clean & paint the U channel and lube the track. when it's all dry put back the rubber strip and put the window back in.. I kept photos of this project, I will try to attach them. Tony