UPDATE:
I managed to solve the Boolean problem on the saucer section. It was a mildly tedious effort, but it was a payoff in spades! It is something I might have to try with other parts of the hull.
By removing the internal extended faces of the Boolean windows, I managed to get rid of the stretch mark effect. Also, by doing that, I was able to apply an internal glow disc to the saucer section. Now the windows look as if they are glowing from within...AND, the light can be better controlled for brightness....the contrast is far better than just applying a glow texture to the saucer itself. AND AND....I can change the color of the lighting...even make it red to show the ship on red alert (ala Star Trek Into Darkness).
