Celebrate your glorious ideas rather than treating yourself as a failure because plots are trickier for you.
Romantic tension is one of those things that's often better managed during revisions, because it's all about pacing.
When you're short on space, a cliché or trope can be the most efficient way to do what needs doing and move on to the real story.
You are totally permitted to just do the fun parts of this and skip the parts you dislike. Hobbies are for enjoying.
There are some projects where artistic urges outweigh commercial considerations, and this sounds like one of those.
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.