Trying to configure everything seen onscreen in that area sure is a problem.
In "Elaan..", it was like this:
Yet in "That Which...", the engineer walks into that same area and it is this:
(much easier to see in the actual episode)
Also, regarding that ladder from EMM, in "Mirror Mirror", McCoy walks to a yellow door that opens to reveal the ladder in an alcove, and Scotty ascends it to EMM.
The way in which he walks to the door would mean that that corridor would exist exactly where the 2 big machines are in Engineering. So you have to cheat a bit to make that fit.
I ended up with this type of setup while working on the 1701 blueprints.
Certainly not definitive, but may help you figure out how it'll all fit in your 3D creations.
Looking forward to seeing how it all works out. Have you decided where in the ship you figure that S2 Engineering will reside?