If I may make a suggestion:
I find this entire thread and the work done in it fantastic, but I might caution one about the temptation to over-think the plumbing.
Fact is, the Enterprise
in TOS didn't have an intermix shaft -- vertical, horizontal, or any other kind. It just didn't
-- it wasn't an idea that was thought up until Phase II
and was then carried forward very effectively from TMP on.
But the original ship -- no bloody A, B, C, D, E, J, NX-01, or JJ-Prise -- just didn't have one.
There's every indication that the way the whole thing worked was thusly:
Notice that everything's going on up in the nacelles. That's where the antimatter is located, that's where the M/A-m reaction is taking place, that's where the warp drive is located.
This idea is perfectly consistent with everything Jeffries had to say on the subject. He kept the ship's exterior intentionally streamlined because he knew that in space you'd want to access things from the inside, not the outside. He knew that the engines (however they worked, and it was never specifically pinned-down) would be dangerous and largely uninhabitable.
Lastly, he knew that as cool as it sounds, you don't have antimatter nor the equivalent of millions of nuclear reactors running anywhere near human beings.
All the really dangerous stuff was going on inside the nacelles. The antimatter was there, the Matter/Antimatter reaction was there, the warp drive was there.
Seriously, keeping antimatter anywhere near crew spaces is a recipe for disaster on so many levels. To begin with, people tend to drop stuff. It's not a problem around normal matter, but even a pinprick around antimatter and the ship would be instantaneously annihilated. And what of security? If it's in the nacelles you can naturally limit exposure to sabotage by restricting access through the pylons. Not to mention, by implication a saboteur must be willing to endure whatever dangerous conditions and/or radiations are occurring in the nacelles.
But a big tank of antimatter inside the ship? One good phaser on overload, and the ship's done.
I can't imagine that Jeffries imagined that they kept antimatter in big tanks inside the ship's hull.
Consequently, all the power is being generated in the nacelles. What we saw in Engineering were power distribution, engineering controls, and other ship's subsystems.
It was emphatically not the Matter/Antimatter reactors themselves.
The Engineering sets that we saw were consistent with this idea. There were the huge tubes at the rear, doing something. Dilithium crystals were needed for something, but it was never clear entirely what.
I postulate this: the power generated from a controlled matter/antimatter reaction is so fantastic that it would completely overwhelm any power systems without sending it through the dilithium crystals, first.
In other words, the dilithium crystals are the ship's step-down transformers. Think of the engines as being like current from the power company: all the 120V AC won't do your computer any good without the transformer that steps that down to a tiny DC voltage.
The dilithium crystals -- rather than being directly associated with the M/Am reaction itself -- are instead power regulators. Or the "energizers", to use the generic TOS term.
It even works to some extent with what we saw happen to the ship when she lost crystals: lights would dim, power would be cut, the ship might not have shields ... all because the step-down transformers were blowing up. Sure, you might run the whole ship's systems through a single transformer, but you better be careful or you'll burn it out.
It's just a thought. I realize that this project is to some extent an attempt to make a ship that satisfies the design lineage, and that's fascinating. However, it probably isn't what Jeffries had in mind when designing the ship.
Anyway, take it or leave it, your mileage may vary, comments, questions, and nasty remarks invited.