Wow, you have been busy! I love the new section you added, it really fills out the story so much more and answered lots of questions! It is really a stand alone story now and you should be very proud of yourself.
I don't have time to do a full review right now, not that I saw too much I was really worried about, but will come back when I can. I hope one or more of the other reviewers can help you out before then.