I agree with Siri Kirpal. I'm not quite clear on what help you need. But I will give it a try based on my hazy impression.
In fiction writing we sometimes talk about "pantsers", who just start writing with no outline or direction and that works well for them, and "outliners" who begin with an outline and a clear direction of where they are headed, while staying open to the possibility that things could change along the way and that works for them.
From what you said it seems like you either started your project as a pantser, or you are not happy with the way your outline worked out. I am an outliner, and while I accept that being a pantser works for some fiction writers, I can't imagine it would work for non-fiction. You didn't say, did you start with an outline and proposed table of contents? If not, there is still hope . . .
If I were you, I would open a word doc and jot down the central themes from each chapter (divided by paragraphs). Then I could look at them all, and with the magic of cut and paste--move them around.
If you are a more hands on person, you could to the same thing with index cards.
Either method would give you a bird's eye view of your book and help you see how you could improve by either reorganizing, filling in holes, cutting, or even doing a bit of re-writing.
Another possibility to consider is that your book is just fine the way it is and you are just stuck in an overly critical mode. No matter what I am writing whether it is a short or long, fiction or non-fiction, I am either excited about what I am writing and feel positive about it (other wise why do it?) or (and this usually comes after I have spent a good amount of time on it) I swing to the other side of the pendulum and think that my writing is a big pile of slop, boring, pedantic, whatever . . . Since I have learned that this is a pattern for me, I either wait and see if the feeling passes, or I ask another writer for an honest opinion. So far, most of my projects (except for blog posts and a short story or two) survive and live to see an audience.
Hope that helps.