This was a super-cool adventure/setting. I had fun reading it, and I think I could run it fairly well.
My only complaint, one that I run into with a ton of dungeons, was that the map seemed so small, the rooms so close, that it felt like the events should bleed together, yet each feels distinct.
I suspect I'd be happier, if the map were just plain larger. I saw 30x12 tiles and thought 150x60 ft, but you reference the USS Johnston, which is apparently about 370x40 ft. To me, having longer, tighter, more claustrophobic passages would reinforce the feel of being inside a ship, where your current map is a bit boxy.
That's my only minor quibble, just a though in case you decide to revise it.
Overall, loved it.