radio shack sells a chaser light kit, rainbow electronics does too, just change the leds from red to orange/amber
and those drawer knobs work great as a diamond shaped panel light faceted stripe rotator effect.
you can also get a blinker driver led for the running lights.
I would just go ahead and make a black paper sealed light box with holes that match up to the window. you can invert colors the image on the window sections , cut an dpaste them onto one sheet and then print them onto black card stock so they match up. its a lot easer than fiber optics or sealing the whole ship for light leaks. metal foil works pretty good, but doesn't stop all the light leaks as you can tell on the bottom saucer third ring join around the middle center.
I also press molded the domes and used clear dead leds for the running lights on the bottom ,with a red led blinker driving white leds and on the top I used dead red and green leds, with a light box and the white blinking ones inside, holes in the top and bottom of the light box.