One of my builds when I was a teenager featured a carefully-drawn top-down view of the bridge based on the FJ Tech Manual. It wasn't a fantastic piece of artwork, but my biggest complaint wasn't the execution, but how two-dimensional it looked. I was never satisfied with the result. If it's too late for lighting, why not try a small, phosphorescent disc. You could "charge" it to glow for a few minutes after exposure, or use a UVA source to make it look like it's glowing.
In fact, you could lay down a variety of fluorescent colors
to light them under a black light, then mask windows and running lights, and coat the rest of the hull of the ship in a UV blocker. When the masks are removed and a UV source is supplied, you'll see only the windows and lights lit up. Of course, navigational strobes won't blink ... unless you're careful with your UV sources and have a blinking narrow beam focused on those with a steady-on source aimed at others.
Then there's polarizing film ... a few years ago, I toyed with the idea of handing out sheets of paper with "blinking" lights on the surface for a bit of futuristic ambiance in a role-playing game I was running. I thought it might be possible to lay down fluorescent ink on a page, then cover selected areas with a polarizing film and shine a strong UVA source through a second, rotating polarizing film
down onto the playing area. The idea being that the sheets would glow like a CRT over most of their surface, but the polarized areas would blink on and off. A neat little magic trick. I abandoned the idea because my early research indicated that polarizing film blocks something like 92% of UVA, meaning I'd have to have a super, super bright UV source to make effects light up through two
layers of film. I don't think there's any way around this, but if anyone makes polarizing film that is transparent to UVA, you could possibly use this to make stuff "blink" on your model. It would be even better if you could get transparent polarizing paint, but I doubt there is such a thing.
And since we're already taking a long walk off a short pier with some of these ideas, I wonder if one could make a small, white-light hologram
of a bridge to stick in the available space. Of course, now you'd have to invest around a thousand dollars in holographic film, a decent HeNe or YAG laser, the laser's power supply, but when you're done, anyone looking into the bridge of your AMT model will actually see a 3D view of the ship's bridge! In a yellowish green tint, of course.
Gosh, this is so much easier when I don't have to actually do the work! I think I'm finally seeing the allure of management!