Yeah, the windows  on B/C deck are particularly deeply recessed aren't they? On my build I cut tiny rectangles out of thin clear styrene sheet, gluing them on top of the kit window inserts with MKK. Worked really well to make them flusher with the hull and I didn't have to worry about adding more MKK due to shrinkage as the MKK dried. I found I could also sandwich the shadow casters in between the window and the clear styrene so they stood out more when backlit.

Before:

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Before Adding Clear Styrene Window Panes by Steve J, on Flickr

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Window Pane Placement with Tweezers by Steve J, on Flickr

After. Just a slight recess:

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USS Enterprise 1/350 scale -  B-C Deck Windows by Steve J, on Flickr