An additional point your diagram has highlighted, with regard to potentially moving the Recreation Deck to below the Cargo Deck - it certainly could not go between the windows, as that spot it now taken up by the engine core! Ah well, maybe further back?
The major reason for displacing the intermix shaft towards the stern is obviously the blue corridor apparently near the bow in TMP
(Andrew Probert hated it because it contradicted the cross-section drawing he did and which Kimble used for the cutaway poster).
But starting near the engine room control console I counted what look like 13 horizontal shaft elements
. Assuming elements have the same length / width how long would the horizontal shaft become before it splits to feed the nacelles?!?
If that would relocate the shaft where Probert envisioned it to be, I'd rather go with that and pretend it's a viewscreen instead (showing a blue corridor) - especially since it apparently doesn't exist anymore by the time of ST II
That piece of footage was actually reused from TMP, and as such bears NO resemblance to the torpedo deck exterior! As a matter of fact, it's not a perfect match for the Engineering Hull either, as the windows are too close to the airlock compared to the full scale model. Time for some more shutter-able windows maybe?
The exterior number "5" indicates Docking Port 5 and that's the number we see overhead in the interior in TMP. However, I find myself unable to explain this:
TANNOY VOICE: Cargo bay to launch crew. Travel pod is now available at dock six.
Some more shutter-able windows [TOS style], no doubt.