Since you asked, would it be possible to have the lights blink more randomly? Also, the bulb shapes might be a little more diffuse..
Yes, I can make the lights blink more randomly. The way they're currently set up, they're all on a 2 second loop, and each of the 15 secondary lights is controlled by it's own unique sin curve over that two seconds. I should probably extend it to, say, a 5 second loop and add more variation to each of the sin curves.
There is probably another way to do the randomization of the blinking. I'll brainstorm and see if I can come up with a different system to allow for far more randomization if the 5 second loop doesn't improve the effect adequately.
More diffuse? I thought I'd made them a bit too diffuse, honestly. In the original effects shots the shapes of the lights are actually a bit more defined.
Go to 3:20 for a good shot of the effect
EDIT: Regarding the direction of spin for the nacelle caps:
At 2:55, it appears both nacelles are spinning counter-clockwise.
At 2:59, the starboard nacelle is spinning clockwise.
At 3:32, the port nacelle is spinning clockwise
At 4:58, the starboard nacelle is spinning clockwise while the port is spinning counter-clockwise.
At 5:28. the starboard nacelle is spinning counter-clockwise while the port is spinning clockwise.
In conclusion, looks like it's safe to say there's no right answer. However, I will be going with what we see at 4:58, since it's a season 3 shot and seems to be in line with the other unmistakable season 3 shots. I'm guessing this is why the latest Smithsonian restoration uses this configuration as well.