"Krystal Klear" and Testor's "Clear Parts Maker" (I think they're pretty much the same thing) would work, all right. My big reservation about them has always been that they sort of "sag in the middle" - that is, as the stuff dries, it seems to stretch away from the center, with the result that the edges are thicker than the middle, and the whole thing sort of domes away from the surface. In little tiny applications such as we're talking about here, though, I don't think that would matter significantly. (Elmer's glue, by the way, will give almost the same effect.)
My own preference is for clear plastic - because it's flat. I've also gotten nice results more than once by using exposed photo film - the black stuff that comes at the end of a processed roll. (Now I'm really revealing my ancient memories. I wonder how many people out there remember the days when you started to take pictures by loading a roll of film in your camera, and couldn't see the pictures until the drug store processed them? Three cheers for digital photography.) But, again, the difference between sheet plastic and those liquid products probably won't matter on those tiny Santa Maria windows. (One tip, though: if you use the liquid stuff, don't follow my earlier suggestion about painting the backs. The paint is likely to dissolve the windows. I know (don't ask how) that's what happens when you try to brush acrylic paint on the stuff. I'm not sure what would happen if you used an airbrush.
Re windows - my thinking is along the same lines as Mr. Morrison's. The phony muntins I'm talking about can't possibly add anything structurally. (If they did, I would have had a serious problem during the past 18 years, since I took all of them out of my windows and piled them up in the attic.) Mr. Dickeywood's comment makes sense if we start with the assumption that the homeowner really wants his/her windows to look like they were made from lots of little lights. My fundamental question is: why would anybody want his/her windows to look like that? I guess the answer is: for the same reason he/she likes phony wire-spoked wheels and a vinyl top on his/her car. Non-convertible car roofs no longer need to be made out of fabric, wheels don't need to have wire spokes, and windows don't need to be made up of little tiny panes of glass.
My father taught architecture at Ohio State for about forty years, and in his latter years frequently complained about stuff like this. He did, however, give me a bum steer on a couple of other vaguely similar, modern phenomena. He ripped two lovely old fireplaces out of the family residence (built around 1912), claiming they were stupid in a house that now had a furnace. And he always held ceiling fans in contempt (in an air-conditioned house). When my wife and I bought a house with a fireplace and half a dozen ceiling fans (every one of which I've had to replace since then - and I'm thoroughly sick of that job), I came to realize that the fireplace and the ceiling fan most definitely have roles to play in a modern house.
I now teach a course in historic preservation and realize that, in the context of the preservation ethic, Dad wrecked that nice old house. (To be fair, the preservation ethic didn't exist when he was swinging the sledge hammer at the fireplaces.) If I were hiring an architect to design my wife and me a house today, it would have at least one fireplace and a couple of ceiling fans. But it wouldn't have phony plastic window muntins.
Interesting stuff to ponder - but enough. This is a ship modeling forum.