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Stock 1989 Supra Turbo w/ Sport Roof
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You might want to enlist the help or opinion of a glass installer. Most every Supra is plagued with leaks in the hatch area either from the glass supports or the taillights. Anything that penetrates the body has the potential to allow water in over time as the rubber degrades, metal rusts, exacerbating the problem. Heavy rain, or washing the car was allowing water to collect in that plastic trim cover at the bottom of the inside of the hatch. I traced the leak(s) to those plastic supports at the bottom of the hatch glass. I used EZR hairline crack sealer that I'd gotten on eBay to solve that problem. It looks like milk and seeps into cracks then dries gummy sealing the leak. I used a small pointed paintbrush and dobbed it on the inside base of those square plastic plugs coming through the metal. I also left some paper towel in there during this process to monitor the leak and to see where it was coming from. Here is a link to another forum detailing what I did. Rust reformer is also latex based. It seals up rust and could also seal leaks where rust is allowing water to seep. On our forum someone was having a leak originating from the hatch gasket pinch weld rotting out and also they replaced the plastic cup inserts that the bottom trim snaps into. Click here to go there. The hatch gasket lifts off easily. It's not glued on. You can check at the bottom to see if there is any rot in the pinch weld, which is common. I repaired mine with JB weld using plastic wrap to keep it formed as it tends to sag until it starts to solidify.
As a JB Weld enthusiast I'd like to share a good tip when using it. Let it set for a little bit (time depends on Kwikweld vs JB Weld etc, and applies to all epoxies really) until it gets a little less sticky before using it. Don't let it harden and cure all the way of course. Helps it not flow out of shape. The plastic wrap is a great idea also! Lightly greasing tin foil works also in my experience.

One more thing, steel-stik works very well for this application instead of the liquid epoxies.
 
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