An interesting revelation in this process: there's a little half-deck between the torpedo deck and the deck above it that makes the decks lineup with the windows.
This reminded me of a thought I had earlier. I wonder if it would help to allow for one undersized or oversized deck at the top of Excelsior's secondary hull, where that thin band of blue / grey circumscribes the hull. That might help out with matching the decks to the windows, as that feature may break up the alignment of a standard sized deck.
Also kind of weird on the all the sharp turns those intermix shafts are taking in the Ent-Refit and Excelsior. Would follow Probert's design, even if it doesn't quite match up with the movie sets.
Really wish I hadn't skipped lunch -- this is sounding a lot more blunt and demanding than I wanted. Unfortunately by brain is really struggling to string words together right now. So, yay, great job, lots of awesome work, and stuff, and stuff...