Just a "Stab in the darkness"...
Make the lumin map the exact same size as the texture of the ship. Then just paint the colour of your lights on it.

Suggest using painting software that suports layers, so you can work with the UFO texture in the background, and then remove the background texture and save just the lumin texture, and then import it into maya, and aply it to the "Incandescense" and you get lots of nice glowing spots on your UFO with the color you put on the texture.

Let me know if it worked!