Chuck,
The plans are based on Jefferies' 947' sizing of his ship.
The deck spacing was carefully taken from the two cross sections he drew -- for TMoST and the Phase 2. In most cases it scales to about one foot. That seems generous, given that the only time we ever saw a "ceiling" in TOS, the decking was mesh -- from the WNMHGB deleted scenes, at the 2:47 mark:
http://www.youtube.com/watch?v=1xe5SUxq25I&mode=related&search=
As for the placement of the decks, they also come from the Jefferies cutaway. This exercise started as an effort to see whether his cutaway and the 947 foot size could work. If you insist the hangar deck as shown be used, it won't. But that hangar was highly distorted for filming purposes, and Jefferies shows how it was intended to look, undistorted, in the Phase 2 plan. I went with that, and only chose to make it a few feet shorter than MJ indicated, in order to avoid having it intrude upon the pylon join.
The beams and various braces are seen -- in this plan -- as part of what is called a semi-monocoque hull. In other words, the hull, boosted by the bracing, carries most of the stresses. There is a rudimentary skeletal "keel" deep in both the primary and secondary hulls -- the pylon joins this -- and the hull is connected to it via the deck structures -- that is why I felt justified boosting deck thickness to a foot in most areas (the mesh decking will show up in a few places in the secondary hull). Given magic materials like "tritanium" that can be as strong as we want, that foot is fine -- for me.