How big are the windows? If they are about 5/16 inch or smaller, you can use that window making stuff. Testors and Micro Scale make it. It is like white glue, but holds together better. Forget which each vendor call it. You use a toothpick and wet the edges of the window first, then add more and pull the edges together. The stuff is opaque when wet but dries very clear.
I have used the epoxy trick where you apply a piece of masking tape over the window. Then mix up the epoxy and from the inside cover the window area. The epoxy will be rough on the outside, but you can polish it because it is flush with fuselage side. Does not come out perfectly, but it may end up better than kit windows.
How much detail is there in that area of fuselage? If not much, painting the inside of fuselage flat black will reduce visibility of flaws on inner window surface.