One more picture before calling it a night.
I decided to give the landing bay and hangar deck a quick once-over... It became necessary to tweak deck levels a bit more, but interestingly, Warped9's shuttle actually fits, IF I adjust the deck below to exactly match the hatch (I'd left some margin around the hatch previously).
Here's a side-view of the whole ship, in section. You can see the landing bay. Note that the bay itself does not run to the exterior hull. There's actually a fair amount of space between the two. This is well-established by the TOS filming minature of the deck, which clearly shows that the doors are significantly larger than the interior structural ring inboard from them... and when comparing the doors themselves (on the 11' model) to the opening in which they sit. I've only "eyeballed" the size of the opening in that aftmost bulkhead, so far. But I'll be doing a bit more analysis as I move forward.