What a major project!
I really liked the atmosphere and I agree with the previous comments that what's missing from this project is basically everything you've put on your to-do list.
That huge creature had me bloody worried! It took me a while to realize that it wouldn't hurt me. At one point I even said to myself, “It's not hurting me at the moment! Maybe if I extract 250 biolum, she won't be too happy!”
In short, a great game! I can see why it took you so long :D Well done!