Thanks guys.
I am re-writing the whole story as I go, and that is a time consuming process of epic proportions. There are over 80,000 words in this story, and I think I just added another 10,000 in the Last five hours.
It is easy to lose focus of the story when you don't work on it for a long time. Even with good notes, it can be difficult to get back into it.
I hope the re-write clears up a lot of grey areas and adds more depth and character development to the story.