The best editors act as therapists and teachers too; like therapy and education, being edited can be emotionally difficult and a challenge to your skills, but if you bring your A-game and ditch your ego, you'll get a whole lot out of it.
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.
There are very few arts or crafts where an important part of creation is destroying part of what you've created. Even sculptors don't have to make the marble before they start chipping it away.
Books often change quite a lot as you're writing them and the book you've written may require a somewhat different protagonist than was called for in your original outline.
Over time, as you write more, you will learn to recognize which ideas can be developed easily, which can be developed painstakingly, and which can't be developed. And you will learn more about your own process of development, which will help make both easy and difficult development go more smoothly.
Even if you didn't have a billion story ideas, I suspect you would still struggle with revisions. It's easy to think of the writing as taking you away from the revising, but don't get too caught up in that love triangle. The relationship between you and revising, between you and the work you've already created—work that you know needs more work—is what's at the heart of this.