Yesterday I went through the whole book, analyzing each scene for its purpose within the story, what the "active" character's goal was, and what the conflict in the scene was. That's a great way to find scenes that can easily be cut or that should be combined because it shows when I've repeated the same "beat" too many times. It also can reveal any major structural flaws in the story.
That's a good news/bad news thing when it happens, as it did. It's bad news because, ack, there's something seriously wrong with the story. But it's good news because usually fixing that thing makes a lot of other things fall into place. In this case, it came about because I thought I was setting up one thing and then changed my mind about how it would all play out, and that means I can go back and act like the way it did work out was what I had planned all along, so I can cut huge chunks out of the middle. Cutting chunks out of the middle is always good. The difficult part is that there are a few scenes related to this plot thread that are essential to the story for other reasons, but this plot thread is what gets the characters into the situations where these scenes can happen. That means I need to find another reason to get the characters into the situations.
I'm having a big "Duh!" moment because this plot thread really does hinge on a character doing something totally stupid that I don't think she would actually do. It's a villain acting like she hasn't read the Evil Overlord list (though, now that I check, this item isn't actually on the list, but it should be). I think removing this element could make for some fun because it makes things more difficult for our heroine. She'll have to do more investigating instead of it being right out there for her.
Meanwhile, I think I need to increase the conflict between two of my main characters. I tend to be conflict-averse, and these are people who probably would really like each other under other circumstances, but in this situation, they have the same goal but very, very different ideas of how to achieve that goal, and one of them can't tell the other what her plans are and that his plans can't possibly work, so she has to sort of play along and humor him while doing her own thing behind his back. That should make her a little impatient with humoring him, which should make him suspicious of what she's really up to. They may eventually get along pretty well when they're on the same page, but at first they should see each other as obstacles.
None of this should be major rewriting, just a little tweaking and massaging while also cutting vast quantities of words. I'll let the subconscious stew over it this weekend and see if I can adjust my mental images and imagine scenes in a new way. It's supposed to be a nice, rainy weekend, which is good for brainstorming mixed with reading. And maybe a little housework. The house is still moderately clean, but I need to do some work to keep it that way.