I'm not certain if these are the plans you were using, but center section of P Deck should be pushed together to replace the center corridor. Otherwise, to get to the port turbolift tube, the car must travel down to T deck before it can get back over to the starboard side of the ship and back on the main line.
Some of the turbolifts are over done. Do they really need so many stops.
Another Problem with the Strategic Design plans is that they show only one sickbay complex (14 beds, but in twok the bed sections were numbered, and seem to go to 28).
The easiest way to fix this is to shuffle some stuff around and lose two transporter rooms:
Copy the red sickbay to over the pink yellow and red circles (with the copied transporter room going over the red circled one) and moving the two yellow circled labs to replace the two purple transporter rooms and adjusting the sizes a bit so all four labs are slightly smaller but you have the two sickbays (which makes sense for a crew of 500) and it still leaves 3 transporter rooms on that deck. The new sickbay would be the primary one (beds 1-14) since it has a transporter room on either side and means the old sickbay is the one, with the far left side being the one seen in the screen shot.
The other problem they also have the Senior officer quarters on deck 4 and normal officers on deck 5, but TMP showed CAPTAIN
Kirks quarters on deck 5 and in TWOK ADMIRAL
Kirks were on Deck 4 (which makes sense, since he was a guest so VIP Quarters in TWOK but in Command in TMP so Senior Officer Quarters).
This can be easily fixed by making some deck 5 quarters for senior officers, continue doing so for the other ranks until you get to the enlisted ranks, and then changing the junior most enlisted quarters into the 9 person bunk rooms seen in TUC.