You'll need to replicate the kit window frame part out of brass strip.
Just make it a little longer so you have a way to attach it to the inside of the outer door. (or you can use the kit vent window part of the frame and keep the kit supplyed part of the window for support...) Yah.. just add some of the little special shapes channel to run the 'glass' in.
To plug the holes use some stretched sprue. Just friction fit them and sand the ends flush.
??? Do the windows roll down on the real race car?