Let's tackle these one at a time...
A few thoughts:
1) Escape pod size. I vaguely remember you having a specific reason for making them so big (was it the discolored panels?) but I still think they're a bit too big.
Shaw's arguments on this matter have convinced me to dump the escape pods altogether. More room for cabins!
2) Power transfer line from impulse engine to power manifold - it seems more logical to have this follow a line parallel to the rear neck line, then bend downward, rather than the odd angles it seems to take.
The angle was mainly to accommodate the turboshaft, but I suppose that could be tweaked a bit.
3) Neck reinforcement - I remember you having trellis bracing on another version. Personally, I see a couple of structural beams as being enough.
Considering the stresses that section is subjected to, and the relative slimness, I figured more than a couple of I-beams were needed. then I decided to put the turbolift maintenance section in there, and also figured some sort of honeycomb structure embedded into the hull would also do nicely for reinforcement, so...
4) Deuterium tank - I would suggest removing the TNG-style tank and using two or three smaller 'pod' tanks that could hold similar volume. More a stylistic thing for me than anything else, as I think it highlights technological evolution from TOS to TNG.
I prefer to look at it as efficient use of an otherwise unusable space, and in a spaceship, every square centimeter has to have some justification. The slush tanks stay.
5) Engineering placement - I suggest switching them, and eliminating the green path from the matter/antimatter integrator running to the nacelle. Instead, have this flow into the manifold, and leave the red path that goes to the nacelle as-is. This would, IMO, simplify it greatly and also allow for an elevator/staging area behind the hangar deck evocative of what is shown in TMP and TFF.
Well, y'see, there's that dilithium doohickey in the middle of the room, and for the plasma to be of any use to the warp engines, it has to go through the dilithium crystals, which means under the floor. Remember, it's not just a matter of efficiency, it's a matter of lining up with what was on screen (which is why, under protest, I included small emergency back-up M/AM reactors in the nacelles, to account for the occasional oddball reference that indicate that the nacelles have antimatter inside).
6) Lower engineering - the one at the forward bottom of the secondary hull. I don't really think this is necessary. Storage might be better use of this space.
Maybe, but the contours of Engineering changed too much between the first and second seasons to chalk it up to a simple equipment upgrade. It's a whole different room. So, my solution is to
really make it a different room, on the other side of the tube assembly, and chalk up the
second version of the engine room to an equipment upgrade (who knows what that area was during the first season) and Main Engineering shifted from the forward area to the aft, with the forward room being kept as a backup, with its primary purpose now being monitoring the main fusion reactors.
7) Antimatter pods/antimatter generator/deuterium injector - I think it might be worthwhile to actually put the antimatter pods below the power manifold so they could eject together, and shift the other two forward so they line up with the other ports. The last small port could then become the tractor beam.
The power manifold is only dangerous so long as the main reactor is running. Dump the main reactor, the manifold is just a bunch of orange tubes. Besides, the fusion reactors also use that manifold, especially if the M/AM reactor is offline for whatever reason. In any case, the components of the antimatter generator setup are all arranged to line up with the markings on the underside of the hull, i.e., the antimatter pods have their own ejection port.
And "The Immunity Syndrome" established that the Enterprise has more than one tractor beam, when Kirk ordered Scotty to put "two tractor beams" on Spock's shuttlecraft. I see the ship as having various types of discreet emitters all over the ship, as opposed to one big honking tractor beam emitter with a fairly limited field of view.
I almost mentioned the sensor pod bay, but I think the setup you concocted works pretty well for something that I don't think was a part of the original design setup.
It does have the advantage of fitting the dialogue of "Court Martial" better than what they dreamed up for those remastered effects shot.
