One part I always struggled with in the past was lining up the sides of the nacelle with the tail section. To avoid that (should have thought of earlier..) was to attach the tail to the sides before attaching the main body of the nacelle, like such;
Finally the saucer, here are the internal supports with the applicable LEDs, and required cut outs where required. I've mounted the supports slightly off centre so that I don't weaken the vertical supports for the positioning of the running light LEDs. You can also see where I miscalculated the positioning...
I'm not going to build the rooms that go along the rim, simply because you can see sweet bugger all through the windows, and that when it's normal scale! (Might be worthwhile on "monster" scale )