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Even if the tail light gaskets are in really poor shape, very little water will enter the trunk -- more likely that the water is coming from elsewhere and collecting there. Is this a few tablespoons of water, or a couple cups of water?
Is there any rust on the aft sides of the fenders that might allow water in? I've seen holes in the trunk floor where it meets the fender that allow water into the trunk... any chance of that? You mention that you have the trunk gasket covered -- do you mean that it's leaking but you're going to replace it, or have you been able to rule it out with certainty?
The holes that the clips fit through along the side of the car (the clips that hold the trim in place) can lead to water leaks too - the factory used a putty substance to seal these up - might check this.
Note about black silicone sealants - pure silicone is probably okay (but it'll make repainting the car more difficult in the future) -- most of the "silicone sealants" offered at the parts stores contain other ingredients which can rapidly accelerate rust.
Best,
Cameron
Rose City
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