Thanks USS Mariner
Some more speculative comparison shots and a side view of the cargo bay/shuttle area. I used the orthographic shot of the Director's Cut Enterprise from Doug Drexler's site for scaling and lining up purposes.
A side effect of the flight deck being lower, I had to push down the hangar deck below it as well to maintain the same height (12') but that also meant that the hangar deck level is lower when it meets up with the cargo bay sliding door lock section. Argh!