If I were trying to fix those windows, my approach probably would be to cut away the frames completely (a five-minute job for an Xacto knife), shave down the inside of the transom, glue a sheet of thin clear styrene over it to represent the glass, and cut lengths of gold, waterslide decal stripes (such as are sold to model railroaders) to represent the window frames. But when you start doing things like that you open a can of worms. If I remember correctly, the windows on the quarter galleries of that kit are compound curves - much more difficult to handle with clear plastic sheet. And if one "fixes" one feature of an old kit like that, where does one stop? Before you know it, you're planning out a project that will take ten years.
On tiny scales like that I actually rather prefer the way Revell handled the problem of the windows in its small-scale Constitution and Victory kits. They molded the window "glass" solid, with remarkably fine "frames" cast in relief. On a tiny model like that it's almost impossible to see anything through transparent windows anyway; careful painting, with a very dark, high-gloss blue or black for the "glass," creates a pretty good illusion.
One major manufacturer, Dragon, has recently been creating quite a stir in the world of twentieth-century ship model kits by molding the planes in its 1/700 aircraft carrier kits in clear plastic. The modeler paints everything but the canopy. Heller was on the right track when it made the stern lanterns of its 1/100 Victory in clear plastic. (The skylight on the poop deck is made the same way, but there somebody goofed: the top doesn't have any camber in it.) We can dream of the day when an enlightened manufacturer molds a ship's complete transom and quarter galleries in clear plastic. But I'm not holding my breath in anticipation.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.