Awesome. You do realize though that you and I are in the minority of opinion about the function of those ports? Most everyone thinks they're windows ... they are, after all, the same color as the other windows. Not that it matters -- most people think it's all just a TV show so what did they know?
Well, most of them ARE "windows." They're just not "sightseeing, viewing windows." So I can live with the them being described this way.
Technically, I can only recall twice during TOS that we actually saw windows on the ship. Once, where there were tons of faces staring in (but Shatner was too busy trying to seduce the last woman on the ship), and another, when we really couldn't see out them (and Shatner was too busy trying to seduce a psycho-actress-type). And in both of those cases, the windows were rectangular.
What I'm doing with MOST of these is having them be little round porthole windows, leading into "broom closets." Inside of those little "closet spaces" are whatever sensors happen to be inside, looking out.
I considered using some of them as "RCS thruster ports" but the positioning just doesn't make sense to me, so I'm going to have covered RCS ports in several locations (behind slide-back hatches, just like the phaser emitters and torpedo tube ends are).
And my apologies if I've missed this, but is it your intention to leave the turboshaft exclusively vertical? I wasn't paying close attention to your Vega because while I found the technique fascinating, the subject of your work wasn't as interesting as this old girl, but I just assumed it had the usual run of turbolift tunnels. Here it looks like just a single shaft in the primary hull. And if you are running a shaft to the secondary hull, will the car tilt and go down diagonally, or do you prefer the more orthodox sidestepping shaft?
Well, so far there's only one lift tube that I know the location for. And I deviate quite a bit from some folks, because I think it's crucial for the crew to actually walk as much as possible, just for fitness's sake if for no other reason. Still, there is a reason for SOME horizontal tubes. Just not the maze of tubes we often see.
So, I intend to have a fair spread of horizontal tubes on Deck 6, with "loop over" connections between the ends of those tubes on Deck 5 and Deck 7. This is something that also came up in Shaw's thread a while back, and he did a fine job with implementing it. I may have a few less tubes, total, but not dramatically so.
Also, with the exception of the ends of the lift chain (top and bottom) I intend for cars to have to "pull over" to a separate alcove, off of the main tube, when stopping. This will allow other cars to move past. I may also have "shoulder pull-over" stops in a few locations in case two cars come head-to-head at some point which is distant from a lift station... these will probably be more relevant in the Deck 6 "spurs" off of the inner region, and there won't be very many of them.
Part of my concern is sizing the lift cars properly. We've never seen any drawing or image of TOS lift cars, except for a few fan-made ones (which I believe don't work). My take on the cars is that they have very little internal hardware, and are entirely slaved to an infrastructure within the starship. That is, they have no life-support of their own (they get air from air which is pumped into the lift tubes), they get power from rails inside the tubes, and they aren't self-propelled, but rather are propelled by hardware in the lift tubes.
That's why I built the "box" around the vertical lift tube you see. The four corners each have "driver coils" in them which propel the car up or down.
The car will have some internal circulation machinery for climate control, a grav plate set (incorporating inertia-control), lights, a control system interface (not an actual independent car control, just a "dumb terminal") and a wireless intercom interface.
Also, probably, some sort of brake system for positive retention at "docking terminals" inside the tube system - cut power, and the brakes deploy automatically, apply power, and the brakes can be retracted.
The trick is to figure out where those various tubes and elements need to be located. And so far, my only guidance is from the bridge set and the single TOS corridor set (which, interestingly, has a lift tube at approximately the correct location relative to the corridor ring).
But in answer to your question... decks 1, 2, 3, 4, 8, 9, and 10 will only be accessed by a single common vertical tube. Deck 6 will have several major horizontal tubes. Decks 5 and 7 will have limited extensions of the system on Deck 6, mainly to allow "looping" without totally subdividing Deck 6.
Obviously, the dorsal will require at least one horizontal "jog" and the secondary hull will almost certainly have a "box" which will be very much like what Shaw created in his version.