Funny enough, I've been playing around with these items
- how to make the bridge module go up and down in height
When I model the bridge area, I'll see if there is enough space for machinery to telescope out the module as it looks like it is just the taller dome sunken into the ship.
- how the impulse engine vents switch between 2 and 8 exhaust ports
This I've played with and the idea is to have 8 ports and various vent coverings slide in and out of place.
- how the main deflector dish grows and shrinks in diameter
I'm torn between blades fanning out from the smaller diameter to retracting outer blades that slide in.
- the retractable spikes on the forward warp nacelle domes
Exactly. Retractable spikes in the forward domes. The domes can transition between opaque and semi-transparent.
- the diameter and height of the lower sensor array dome on the primary hull
I haven't noticed this before. Is there an episode that I can check this against?
- the markings near the upper edges of the primary hull which appear and disappear
Are you referring to the black arcs near the port/starboard lights? If so, there would be hull panels that slide out of the way to expose them.
- the "NCC-1701" registry markings on the ventral side of the primary hull, which change orientation 180 degrees from time to time
This one I've read about. Is there a specific episode where the registry flipped (as in showing both ways in the same episode)?
- Here's another one: The windows from the Observation Deck in "The Conscience of the King". There are no matching square windows visible on the external shots. The only thing I can do here is assume that like other windows on the ship, they have a shutter ("The Mark of Gideon") and when closed, makes the window blend in on the exterior.