I've been fascinated with this movie ever since I first saw it, which is why I made those models in the first place back in the early 80s. When I started I, like you, had little to go on apart from multiple viewings of the movie, hence some of the mistakes I made in passageway and hatch dimensions. I figured much the same as your decks, going by the blueprints that have appeared online; those for A & B decks I posted further up this thread in case you hadn't seen them. A Deck was built as a complete set as you know, including the bridge, galley & Autudoc, but in one of the deleted scenes Ripley is seen descending to the level of the Autodoc apparently from the bridge, which suggests the Autodoc was intended to be on B Deck, which would make sense as it would then be on the same level as the main airlock, and would avoid the need to cart Kane between decks. There is also the contradiction in another deleted scene of when Parker & Brett go off to make the cattle-prods. They scoot off down the passage from the Galley to the T junction of the passageways from the Autodoc & Hypersleep chamber. But as there is no other passageway or room in that direction, where were they going? These inconsistencies suggests to me that after building the A Deck set, it was then decided to deliberately not show certain parts of it so they could be imagined as being in different parts of the ship and not all on the same level. This also suggests there were four decks not three, but on the Mother screen the legends A Deck B Deck & C Deck are clearly visible, but there is no D Deck legend.
Like with the apparent contradiction of Parker & Lambert descending into open space through the bottom of the hull, and the discrepancy in the orientation of the landing feet, the interior sets and spaces don't match the outside dimensions.
As B Deck is only seen three times I think; when the crew go below following the facehugger's leak; in the sequence where they do the initial search for the small alien; and when Parker, Lambert & Ripley go towards the shuttle, much of what this deck housed is never shown or described, so we can only speculate on it's uses and functions. In one image I found of the outer main airlock set, it is quite clear that the science blister is also on this level, as it was built at the same height as the airlock, overlooking one of the landing legs. When I can I'll post that pic too.
I imagined C Deck was the maintenance level, with the passageways full of machinery, where the vehicle 'garage' is where Brett goes chasing the cat, and the engine control room where Parker & Brett are seen several times (and where Ripley sets the self destruct sequence). I'm sure you know this was the Autodoc set and passageway heavily-redressed. There must also have been some kind of workshop onboard to make minor repairs. This was hinted at but not seen, and I imagine it would have been on C Deck. When I posted that speculative drawing of a maintenance workshop I envisioned it as being on B Deck, but now I think it would be better suited to C Deck.
Something else I've just thought of. In the sequence where Brett goes into the landing leg room after the cat, in the one scene another set of landing legs is visible as a silhouette in the background. They then must be the rear two landing legs. However, to have them visible to each other means they would have had to be so far up in the outrigger nacelle sections, they would have been above A Deck and if you look at the height of the extended legs and the height of the nacelles, there wouldnt be enough space to accomodate the height of the legs. Another example of where the interior sets and exterior shapes don't match. With Ridley Scott repeatedly saying he's a perfectionist and he must have shots right, how did he make these apparent glaring errors? In the words of Toyah Wilcox: It's a mystery