So, while the last picture renders, I will post my progress for the evening.
I set out to frame the secondary hull. I first started by trying to extrapolate from the plan decks a circle at 2m intervals along the length of the hull. I wound up with wildly varying hull contours, so I abandoned that attempt in favor of selecting a custom extrapolation from the contours of Q and R decks (Q deck is a little above centerline, R deck is a bit below centerline). Once I had the hull contour (which I took to be the inside edge of the hull), I created slices at 2m intervals running perpendicular to the axis of the hull, so I had a series of rings spaced 2m apart from front to rear. I added supports for each deck, and incorporated them into each ring. I only got as far as the aft end of the shuttle elevators, but I am happy with the progress so far.
As I expected, quite a bit of the structure on the decks is either too far inside the hull, or too far outside the hull. Once I have the hull cross-section framing completed, I will reposition what I can to be inside the hull (or remove it all together). Once that is done, I will go back and add the fore-aft framing. The exterior hull is far more easily generated from the original contours I used to generate the frames.
First, the wireframe fore and aft:
And the renders:
As you can see, Main Engineering is a tight fit. I may end up dropping the whole deck a bit to make things fit better.
The last picture finished rendering while I typed.
I will almost certainly wind up cutting out some of the "slack space" between decks that are in the current design. Most decks I can reduce by almost 1/3 and still fit what has to be there.