I'm not going to lay out each deck in detail. Firstly that would get very involved and I don't think I could think everything out thoroughly enough to be credible.
This cross-section will be largely representational and to some degree fluid for the sake of future creativity. What I want to do is use the description given in TMOST as a general guideline going forward. From that, my own perspective and feedback from others here I can establish where certain specific things are: officers quarters, main lounges (I'm sure there would be smaller ones as well throughout the ship), Sickbay, main transporter rooms as well as bulk cargo/evacuation transporters, Main Engineering, the Bridge and Auxiliary Control, Shuttlecraft Flight Deck and Maintenance deck, fore and aft photon torpedo launchers, ship's phaser arrays (3), navigational deflectors and main sensor arrays. Maybe some other things. The rest of the layout will be more vague in terms of description.
One thing that needs to be established is the nature of the engineering layout. The choices are between the TOS template and the TMP/TNG template. Having large energy conduits running up to the impulse drive as well as the warp units cuts into a lot of space. How and where is main power generated? How is delivered?
Two past problems are avoided with this design. The torpedo launchers are well clear of any main power conduits unlike that of the TMP refit. Also because of the width of the secondary hull the hangar doesn't intrude into the space where the pylons are fastened to the secondary hull.
The Bridge, Main Engineering and the shuttlecraft hangar facilities need to be designed in more detail to fit them properly in place. And the hangar area can't really be done in much detail until I actually finalize the shuttlecraft.