I'm afraid that TMoST suffers from the same inconsistency as the series itself. The deck descriptions and the cross section were done by different people and don't agree. And in the cross section there is no 2 story engineering space that we ever see in the series. it has things drawn in that we never witnessed. I'm sticking strictly to the text description of the saucer because that is what the TMP crew were using (by way, I think, of Franz Joseph). TMoST never describes any other deck contents, only saying that the secondary hull was given over to engineering and the hangar. So there I have made use of the cross section, but only so far as the contents go. For the decks I have gone by the windows on the exterior which create a different deck layout. The series itself is even more vague than TMoST and the only thing we ever get in the series to indicate where season 2/3 Main Engineering is comes in the way of a special effect from The Day of the Dove. And we all know how reliable the special effects were. Still, that places it on the same deck as the TMoST cross section does, although a bit forward.
I seem to remember that different episodes used different deck designations for the same location. And with 3 different descriptions of the interior, it isn't surprising. We have Matt Jeffereis cross section which shows 9 decks in the saucer, the season 2 writer's bible listing 11, and the season 1 writer's bible listing 20. So in any episode with a deck reference you have to ask which version they were going by or did they just make it up and did the staff writers bother to correct it. My understanding of Roddenberry's main rewrite focus was to make the story work for the series and be outstanding. So how often did they bother to correct technical details, especially when one of their stated goals was to be vague and leave things unexplained. That is why I don't hold to a strict interpretation of everything in the series. They were using a different standard. It would drive the Thermians insane to try to reconcile all the contradictions. 20 years later when TNG came along, they realized fans cared about those things so they started keeping better track and making things more consistent. I think they Thermians could make an ENT D and even the Refit, but the TOS Enterprise would have them squabbling over details like we are. Without the outside sources and later canon to go by, a lot of these things just have too many variable answers.
I long ago ceased to imagine that there would ever be a consensus on some of these thing, though I had never delved into all the various ways the engineering systems were referenced and that is even more confusing that settling on the length of the ship and how many decks it has. And my project is not just one ship. I am trying to work out the systems of 5 ships simultaniously (TOS Ent, TMP Ent, TFF/TUC Ent, TSFS Excelsior, and Ent B). So I'm looking across a span time (3 years our time, 100 years Trek time) to fill in the gaps and produced somthing logical and functional. I've only glanced at the NX-01 design and left it alone as it is an older system. They only thing I took from it was the horizontal nature of the warp core (which seems to be supported by That Which Survives). So many of the creative drawings of the TOS Enterprise internal systems fail when you run them through the gauntlet of what we see on screen. Even Doug Drexler's drawings for In A Mirror Darkly don't line up with what we see in the show (he has the pipe cathedral as part of the warp drive with the pipes angled the other way and butting up to the hangar). So even in that last appearance of the TOS design we have some further differences. They also gave us some additional sets, which no one in this thread seems to be using (including myself).
I'm hoping in this thread we can continue to whittle down the number of possibilities to something reasonable that can inform the projects we are working on. My drawings are mostly of the equipment, not the function, so I hope my drawings will be like the TOS Enterprise - adaptable to many theories.