I'm reading, too, I just haven't had a lot to say. You cover everything pretty well.
Regarding deck alignments:
1)Personally, I find the idea of a 'symmetrical' secondary hull (i.e. one which has even deck spacing) rather appealing and that does seem workable from your model with some slight tweaks. The 'lower half' (below the hangar deck) already pretty much is, and with some equalization of the upper decks and shifting slightly upward, you might have it.
2) I don't think the decks in the neck really need to line up with the decks in the lower saucer. I might argue that a small 'halfsie' non-deck (for separation bolts and such?) at the top of the neck might make the areas there line up generally better and possibly allow for more even deck spacing.
Those are just minor nitpick thoughts.
Overall, I think you're doing a good job and addressing everything pretty well. I'll try to chime in more if it helps.