I preach all the time about using highlighters or markers to hone in on one thread of the story, the hero or heroine's conflict, or their growth arc. It's a neat, clean way to to focus on one part of the story -- apart from everything else -- and make sure it works. Because writing a book is a lot like braiding, one story line overlaps the other as a third story line twists around those two, it's sometimes hard for us to imagining pulling one thread out, examining it, making sure it works...but, trust me, sometimes it needs to be done. As in the case of my recent hero who needed to be tormented more than I'd tormented him. :)
Still, this goes beyond "needing to be done." When you're working to make your project the best it can be, you owe it to yourself, your audience, and the project, to give it your best. And sometimes that means putting every aspect of the story under a microscope.
I'm here to tell ya, it's not hard. LOL Print your document and use a highlighter to illuminate an individual thread and then focus only on that thread. The first thing you're going to find is that because threads are only a "part" of the story, they're not long or hard to follow. The second thing you'll see is how easy it is to spot both errors and successes. In an hour or so, you will have not just followed a thread, but you'll either have approved it or fixed it.
And in the long run, you'll have a better book.
Happy Monday...and Happy Reading!