Could your reclarify for me which one is scaled so that the deflector dish size is the same for both the Excelsior and refit?
Here are some of my thoughts after reading this thread, although I skipped some of the history chapters, etc. I wish the original poster were here to respond to some of these thoughts, as his/her ideas were really interesting.
Great that you tried to address the variations used in the show. I like the idea that the Centaur and Mediterranean are the same class, just variations. We should consider that canon.
I imagine NCC numbers working such that the next ship of the same class/type/whatever after 2099 could be 20100, instead of 2100, meaning that Excelsior numbers could cover a lot of years, and that there is no need to account for the jump from 3000's to 10000's in the registries that has very little filling it in.
I suggest that the reason for low and high registries serving together and that TNG and DS9 show ships of various eras all at the same time is simple: If a ships is lost, Starfleet replaces it with one of a newer design era, and otherwise just keeps upping the amount of ships in the fleet with newer designs as they come out. An Excelsior class
USS Yorktown could be replaced with an Ambassador class
USS Yorktown, but if the Excelsior class
USS Yorktown survived, it would just still be in service as long as it could be kept in operational condition.
The Ambassador serves as an example to me me of what an uprated Excelsior could look like, filling in more of the unused space that many have mentioned could be there.
I think the USS Dallas depicted the warp core as being in the bulge at the base of the wings. To match with the warp core ending at the Impulse Deflection Crystals, it would make more sense for it to run vertically through the center of the ship, maybe even give the vented neck a purpose of generating a field of some kind. On Trekyards, Probert explains that the vented nacelles (which glow blue on the Galaxy) were carried over from the Excelsior even though he did not feel he had knowledge about what the vents would be able to do.
The Pen-nacelles have this blue venting, too, it is just painted on.
How about a dual-core design, with two cores side-by-side, one TMP-style swirl chamber and on TNG-style reactor? The TNG-style one would be added later. One for each Impulse Deflection Crystal
How about two swirl chambers in the center of the ship, and then a TNG-style core in the bulge?
I read a comment about the power transfer conduits and how they would split. It seems to me that there would be a single conduit out of the core that would split at the bulge. This is sort of like how the power transfer conduits head in different directions at the end of the swirl chamber at the back of the engine room in TMP. In TNG the split happens right at the vertical part of the core, an advancement in that the horizontal part of the system is not needed, and perhaps the reason that other terms that were used early on got changed to "warp core."
By the way, what is the second tall structure running behind the warp core in the TNG engine room? Would the Excelsior have one?
EDIT: I note in the linked images posted a couple pages back that the fan designed engine room has tow of these extra structures running up the back of the warp core and that they have some TMP-style connection detailing. Depending on what they do, Could these be the two structures running up to the two impulse deflection crystals?