You ask for the bones of plot, but it sounds like you already have those: start, middle, end, some drama. What you need are the muscles and tendons of plot, the pull and thrust and tension that turns a skeleton into something that moves and breathes.
Satisfaction comes from sustained tension leading to a climax. The tension in a mystery is usually an unanswered question: who, why, or how.
Today is the fifth Tuesday of the month, which means that my answer to this heartfelt letter is available exclusively to my Patreon patrons.
It sounds like going scene by scene and character by character has been helpful for you to this point, but it's not what you need right now. You need to see the novel as a novel, to grasp it in its entirety and understand not just the individual parts but how they all work together. You need to turn off your engineering brain and get the book's gestalt. And how you do that is: you read the book.
Being a doormat is not something readers generally find appealing in any character, and particularly in a main character. Give her things to do and let her do them. Let her take risks and sometimes succeed and sometimes fail. Let her pick a goal and commit to it and pursue it. Let her, as you say, make choices. Otherwise she isn't really a character; she's exposition with a face and a name.
Book middles frequently involve beloved characters being in serious peril or coming to harm, a proliferation of plot threads that can feel out of control, or a mess of problems with no apparent solution. These are things that can be genuinely hard for writers to face, just as they're hard for characters to face. It's so much easier and more enjoyable to focus on the beginning, when everything's fun and exciting, and the end, when all the questions are answered.