Hey, I fixe my window were it leaked and a couple weeks later it leaked again. I took everything apart and had a buddy pour water while I at inside. I had a small tear in the fabric all the way at the bottom. The top guy told me he couldn't put a patch down there. I went to a boating supply store and they had patch kits for the boat tops. Used that on the inside, and put silicone caulc on the outside. Then I left it in the garage for a couple of days. That fixed the leak for now. Now I'm saving back money for a new top. Found a top guy that does side work on the weekends. He will put a new top on for $600. One of the guys in my Mustang club recommended him and had used him in the past. I should have a new top in a few weeks.

 

About a week ago I too noticed for the first time, a puddle of water in the well behind the rear seat after a heavy rain [groan] Because the area is a bit dusty (lol) I think I noticed a water streak flowing from what looks like the corner edges of the rear window so, that's where the water is probably gettin in.. Gonna try dabbing in some hot glue there to see if that plugs the leak!

 

Mine is going the same thing. I used clear silicone, it worked for a couple weeks. It's not AS bad as it was, but still has a little leak. Going to clear that silicone and use some hot glue or some Marine Adhesive.