I'm looking forward to your corrected visualization of the skull cabinet with interest.
Another issue I'd like to address is the sickbay door frame. The frame part (nearest to the main corridor) either extends too much or the entire partition wall needs to be thicker
Here is a screenshot from "The Ultimate Computer"
that hopefully illustrates the problem I'm having.
Then the back wall of the transporter room shows two turbo lift options although there was never more than one in the actual footage.
My scepticism towards the accuracy of the "Journey to Babel" plan has increased over time. Where the set parts match the Season One plans you mentioned, I'd think we are on the safe side but for the other areas these should be double-checked, IMHO.