Hope this isn't too far off topic Shaw, I know you don't want to "fill in the black boxes" too much, but since the following bears on the inner structural relationships, it's something I thought should at least be discussed and gotten out of the way, before moving forward.
Food for thought? Since we are all agreed (I think) that Jefferies TMOST cross section is a lot more representative of what he intended than most people previously thought, what should we make (if anything) of that little doohickey he put just below and in between the necelle pylons and the dorsal? My guess is he intended it to be some component of the engine system itself, possibly the engine (reactor) itself, or the housing thereof? We can see by comparison with the Phase II cross section (see below) that Jefferies left a cavity or bay, in the same area, and its perhaps interesting that in this case, it's right where the engine pylons themselves attach in this new version!
Given the perspective corrected length of the cathedral tube chamber, it's unlikely this feature could be the same thing, so it must be some other part of the inner workings?
So anyone got any ideas as to what it might be? I know we're just seeing the cross section of it, so it might extend deep into the hull, we just don't know, so there are lots of possibilities to think about.
So perhaps this could be one of your "puzzle pieces" Shaw, included separately, along with other internal odds and ends, that could be made use of, or ignored, as aspiring starship builders see fit?