We have a Nauticat 39 (UK based) of 96 vintage and had similar problems with window corrosion
and then leakage.
The leaking which we had was not caused by the window seals
but was caused by corrosion
between the alloy frame and the stainless screws. We replaced all of the pilot house windows as we had corrosion and bubbling of the alloy (which was starting to crumble to dust) between the alloy frame and the rubber seals
. The new window manufacturer, Ertec, described to me how these old windows corrode from the inside to outside though I can't rememeber all of the details now. Here is a picture of the centre window showing the corrosion and leakage:
The picture is looking up at the bottom of the window (from the galley
steps) and you can clearly see that the corrosion has come from the screw holes.
We had new windows made in Denmark
(the original maker no longer exists) but the new firm have the patterns for Nauticat boat windows and can make from their plans though it mis necessary to confirm dimensions and, importanly, wall thickness.
It was significant project
although not difficult, I have a whole suite of photos that I could share with you if that was useful as well as the experience of doing the job and all of the contacts with Ertec in Sweden
. Respond here if you want more, I will check back in a few days.
We had grey tint glass in the new windows which is a big improvement for glare reduction and it does modernise the look of the boat, see before and after: