There may be another, less drastic solution to your problem which I implemented when I had a slightly leaking window. This process doesn't involve removing the windows. First, I excised all the rubber gaskets with a utility knife and a curved blade, both on the outside and the inside of the window frames. Then I masked the area around the frames with tape (there're tapes you can find in artists' shops that do curves) and I pressed Sikaflex 295UV with a caulking gun, smoothing it out with a gloved finger or a thin spatula. As the name suggests, this kind of Sikaflex has great UV resistance and it's used for sealing hatches and windows in boats. Make sure you remove the tape immediately afterwards as it dries quickly. This means you have to do one window at at a time. It's good to repeat this process on the frames that are inside the boat as well. It's a bit labour-intensive but it works well and the costs involve only a roll of tape and a tube of Sikaflex.
-Nicholas
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