You're definitely going to have to build up the "torpedo superstructure" part of the neck before you can really figure out Engineering. I'm sure that the ceiling lines will be different than what was seen in the set, but not dramatically so, I suspect, and I'm pretty sure that the majority of it will fit reasonably well (the major exception being the forward corridor, of course, but you already know about that!)
On thing I find myself wondering about... and which I suspect might require Engineering to be at least a deck lower than is generally assumed... is the intersection of the nacelles. It's very clear that the intention was for the "vertical runs" from the horizontal engine core to go straight up into the pylons. I wonder... what level (in your model) do these lines intersect at? With a CAD model, it's pretty easy to determine that sort of thing... and that would be central to my placement, were it me doing this project. I suspect that the various people who worked on this may have gotten it wrong... Kimble, Strategic Designs, even Andrew may have made a little "snafu" there... hard to say for sure without doing the 3-dimensional stuff.
If you end up having angled "vertical runs" that pass out into space, or require a "jog"... ANYTHING other than "running up the centerlines of the pylons... there's a problem, as far as I'm concerned.