Extremely fun project here. Its a little old and outdated compared to the modern material on the web to use. As someone with a very good background in drafting and design, I have to weigh in here.
The first issues are in the saucer. Using all existing plans based on the original models, you are missing the correct thickness in the middle of the saucer where it slims down to the actual 2 deck disk. That should actually be 3 decks thick. 2 full dimensioned decks, with a 3/4 height deck below and a 1/4 height deck above to be used as conduit routing and thruster fuel storage.
From what I have seen the only vessels that had the photon torpedo system in the TOP of the saucer was enterprise in the original "cage" pilot and the pre TOS ships with single warp nacelles.
The dorsal neck is not used to contain a warp core. Its sole purpose is a turbo lift tube, an emergency stairwell, deuterium feed lines, cargo storage, power conduits, external umbilical connections.
Even all cannon and non cannon single nacelle ships all have the dorsal connector as being storage and power conduits. Just look at the famous screen captures from when the Enterprise escapes space dock in st3.
The warp core was always a tennis ball in a tuna can shape for everything before the motion picture. The official data for Miranda/refit/ excelsior states the modern TMP and later "stick" warp core as being a completely brand new just released design.
The two triangles you see in main engineering are the top of the reactor sphere ( much like the actual prop shown in "into darkness") and contains matter/antimatter injectors and the actual dilithium crystal holder.
the D7/D7c double warp core arrangement is basically this sphere being fed by two separate warp cores similar to what was used for nx-01.
And the tennis ball design is further proven to be correct because in the final season of Star Trek Enterprise they did alternate dimension episodes where the crew ran amuck trying to take over the constitution class starship the tholians captured in the original series.
And in those episodes, the tennis ball reactor core was proven as cannon, and the three plasma conduit taps from the reactor core were shown for the first time. And they look a lot like some internal cross sections on the net.
monte jon Julio new paradigm studios blueprints show it awfully similar to what the ST Enterprise episodes show.
And there was no ejection system for the warp core pre TMP. It was built into the secondary hull. Its why the saucer separation exists. And no escape pod system either. The primary hull is the escape pod.
A lot of the build issues are from the wonderful use of combining so many different off scale blue prints form the internet. Even when looking at the original TOS film models, they had serious scale issues between them all. One comparison study showed 3/8" difference in the nacelle diameter.
I believe part of it may have been from accidental damage to the film models post series cancellation.
Also a lot of the size issue in the secondary hull seems to be from the prints shown, seem to be based off a few REFIT blue prints for the Enterprise A that currently exist online. They do look nice for internal looks, but the refit changed everything internally forward of the bulkhead contained the entrance doors to the shuttle bay.
Also it looks like you forgot to calculate the hull thickness in as a variable. Ive spent a lot of time looking at enlarged copies of the blueprints and under sufficient magnification youll see how the lines change thickness in the back half of the secondary hull.