I rebedded the windows in my old 1977 42' Californian. They were trimmed with wood vs aluminum, but I found this article from the late David Pascone very helpful, anyway:
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https://www.yachtsurvey.com/WindowRepair.htm
Just to be clear why I was offering this up...
When the boat is underway, there is, by nature, a lot of flexing of fiberglass and some flexing of wood -- but extremely little flexing of glass. When it comes to sealing something rigid to something flexible, the old saying, "The bigger the glob, the better the job" often applies. The amount of movement the seal can accommodate is often related to its thickness.
A thin, cosmetically pleasing bead of sealant, under perfect conditions, isn't super likely to be able to take the flexing for a long time. When one adds surfaces that are, to some extent, contaminated and degenerated, the odds of a long life go down even more.
So, I don't think you are likely to see complete success for a long time by sealing the windows from the outside. If you seal the window-wood interface, I think you'll still get water via the wood-house interface. If you seal that, the wood-wood interface on the frame. And, in some amount of time, even where you did achieve a seal, I think the seal will start to fail in places.
I'm also suspect that the leak didn't start when you stripped the varnish. Instead, I suspect that it just got a heck of a lot worse at that time and became noticeable to you.
Many of those Californians (and similar trawlers) have slow leaks that get the wood around the window damp, then it softens, then it rots and/or the termites find it, then it weakens some more. Then things flex some more. Then one really starts to have it staying really wet on the inside, discoloring the interior wood, or even water just dripping down the inside of the house in heavy rain. Ewwww. But, really common. How many boats have you seen with stains under the windows? They began before they began, and once they were thought to be bad enough to address -- they were too far gone to address easily.
I'd do, as I did, what Pascone suggests, which is to remove the outer trim, remove the glass, clean out the caulking, and rebed. It really wasn't that bad a job, except for the number of windows involved (and I didn't do them all).
In my case, I didn't always fully rebed. In most cases, I left the glass in place and cut out a ton of the old sealant and anything that looked bad, then rebedded it in place. Then I covered the fiberglass house with masking tape and the surface of the trim with masking tape, applied more sealant, and squished it right down and screwing it in, wiping away what squeezed out. It solved the problem.
