For now I am going to consider the skull cabinent solved. As to the door between the Examination Room and the Bed Ward I'll check into that this evening. My read from the plans is that wall/ door is 6 inches deep. WARNING: any measurement you see on my copies of the drawings on on any of the first study models I've built do not reflect true measurements of the panels but the exact measurement from divider dead center to divider dead center. So to adjust for what you see subtract 1 inch and 1/2 for the spacer between any of the panels to get a true measurement for the panels on my models.
As to your concerns over the 2 turbolift doors in the corridor at the back of the Transporter Room. Try to think of the Stage 9 plans as a tool to plan the variety of options on how they wanted to dress out each part differently to represent different areas of the ship. Although I do subscribe to the inboard Sick bay Med Lab related sets as all interconnected, I do not hold the same view for the outboard sets being representational of where they sit in the ship due mixing and matching details like you mentioned.
Concerning the previous 2 sets of plans...I got lucky. In the areas of the new sets they are for the most part a close representation of what was standing. But the 2 prior sets are not accurate when it comes to the transporter chamber given the larger number of pads seen in those drawings.