I agree. My cross section based on Jefferies' plan was meant to serve as the beginning for such a project. I don't have much use for some of the internals in the Booklet of General Plans- nonsensical connections of parts like the pylons, nothing behind the main sensor/deflector, screwed up hangar deck, etc. But fix the nonsensical stuff and maintain his exterior design and call it Achernar or Constitution or whatever. It still is a cool piece of work.
I'd just have a parallel set of plans that is closely based on Jefferies and what we saw, with some reverse engineering from Phase II and TMP.