The  ideas I had on the 10/26th were just too difficult to implement.  The inside of the nacelle is too small to build a shield between the sections.  I've decided instead to simply use some mylar paper and bend it around.

     The  yellow lines in the picture above indicate the mylar paper, laid once in the front of the nacelle so the red LED doesn't blow through the plastic, and another behind the red LED to prevent blue and red light leakage.  The blue LEDs are stuck to a frame, pointing them straight up to the mylar stuck to the top, reflecting the light.

     The port / starboard indicators will be driven by the LEDs directly, their junction sealed with glue and shrink wrap tubing.

     At this point I have masked the edges (for gluing) and have painted them black and then silver.  I figure the light shining around will prevent there being three distinct blue light sources when viewing the warp coils.