What I'm saying is not to rely on the TMP design, but the TMP design came from the three seasons and 2 pilots of TOS. So if we know what the TMP design is, we can know which of the episodes they were basing it on. I think the two designs share similarities that aide in understanding each. I would say of all three seasons that That Which Survives has the most detailed information on the TOS system and it parallels the TMP system. I believe it was Mike Minor who came up with the new vertical engine core. He also was just going to replace the warp nacelles, pylons, and deflector dish and leave the rest of the ship the same. That is kind of where the design went, but they kept changing more with each iteration (Jefferies, Taylor, then Probert). They pulled the mystery elements out of the shadows and put them on full display as the main focus of the engine room. Far better than the mystery pipes they never explained. And as someone had pointed out, the TMP design was lacking in several areas that we can pull from TOS to flesh that out.
And one of the things to bring up is the cross section that Jefferies did that was included in TMOST.
I colored in three areas. Red would be main engineering. Gold the pipes structure (assuming it isn't highly forced perspective, which he really didn't leave space for). The blue is an odd structure. It is a short vertical section with a big box on it that sticks into the deck below. I have decided it is a horizontal plasma conduit, but it could be the pre-cursor to the vertical shaft we see in Phase II/TMP and onwards. Of course there is that larger vertical shaft that goes clear through the engineering hull that could be that as well (though the engine room doesn't fit in front of it). This was the first thing I looked at when trying to figure out this ship. In analyzing the layout, I determined that the scene where we meet Sarek and Amanda in Journey to Babel could not take place on either side of the hanger so it must be in front of the hanger. The set design agrees as the back wall is blank (looking down the length of the hanger you would see the doors and for a set that wasn't nearly big enough, just being blank works). That is also the only deck Jefferies left that the engineering room would fit in the entire ship. I put a red box around the area engineering is often put to highlight that there is no room there. Jefferies would have included one of the most important sets. Now I won't claim it has to be the red area I picked, but it would be that deck according to his plans. And in case you are thinking that is just a rough sketch of what Jefferies envisioned....
He kept a virtually identical internal layout as he worked on the Phase II Enterprise a decade later. So the room spaces are not an accident. Between Taylor and Probert, the engine room move up and forward. But at this stage it was still Jefferies work and we can see that much of the internal layout is the same. I consider this to be more significant that the text in TMOST for a lot of things, especially considering designer intent. And Jefferies did work on TOS right through the final episode. I feel confident that the season 3 episodes we have been discussing were cleared with him. He probably designed the set redress for the crawl-way for TWS.
Anyway, that is some of where I am coming from. I love blueprints so when I learned how simiar these two were before Phase II became TMP, I decided to base my decision a lot of Jefferies original cross section (with the hanger from the Phase II).
There seems to be a lot of empty space, so, I assume the voids are filled with unexciting equipment not worth being in the drawings, except the room air conditioner - very important on hot days. 
The hatch were Scott and Kirk place the antimatter is not present in the Mandel drawing, but there are antimatter operations is a room behind the hatch - must have been dumbed down for cartoon consumption. Based on the Mandel drawing, all the warp action is done by the rear magic sphere labelled "space-warp generator" - nice and compact. This drawing must have done before the concept of the TNG warp coils. Overall: 
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Downloads of the sideview picture is locked up from that site, so, I can't get a copy of the photo to use, I'm switching to the Sinclair drawing and any other Kerr stuff I can find. Thanks, 
