Excuse my posting twice in a row. I didn't want to mess with editing my previous post while others might be replying to it.
Anyway, Andy Probert got back to me and here's what he said the features were intended to be.
The cyclopean eyeball above the bird logo was left off the studio model, it it's where the bridge was designed to go, as below...
Andy Probert (via email) wrote:
Shuttle bay: Look on the plastic model and see the indented area on the top of the aft end,... that is the landing bay door. [Looks small because size was reduced somewhat on model]
Impulse engine: Omitted by a tight schedule, yes, but it would have been recessed into a vertical slot starting just below that landing bay and ending symmetrically below. The reason there are few (if any) side windows at the back area of the ship is because that's where that engine & power plant would have been.
Wing spacing: The wings were to have had a LOT more substance to them (as seen in my drawing) but was reduced [on] the model. They are separated to allow the engines to 'see' each other and generate a warp field. As previously noted on the board, I did not design the subsequent ships that ignore my attempt at requirements-for-warp-drive continuity.
Main warp engine room: Is in the dorsal 'hump' just aft of the twin disrupter mount and you can see an indication of the energy conduit shielding running down to the warp engine in my calendar painting.
Life boat covers: Yes, they were duplicated on Drexler's beautiful little shuttle (warp engine rule aside), for visual continuity.
Nav Deflector: Again, it isn't a weapon, just a deflector...
Disruptors: Yes, I did mirror the two top aft weapons on the bottom.
Cargo Bays: At the leading edge of the lower 'wing'? Yes. They've always been cargo doors and my original design included large central areas to house cargo & other departments but was truncated, for some reason, when Greg built the model.
Note the built-up detail on the lower wing behind the cargo bays, as mentioned above, and the much more prominent "hunch" in which the engine room was designed to go. You can also see the bridge detail on this sketch.