Revising is as individual as writing. There's no wrong way to do it, and there are no hard and fast rules about how it goes.
The person you injured is you, in the sense of costing yourself the time and effort of repairing the problems with your work, and the person you need to apologize to is you.
Drafting is engineering and construction. Revision is art and design.
You already made your work in the best way that you know how. Now you need editorial advice. That's part of the process for any writer, and being an editor in no way exempts you from it.
I love semicolons; they're great. The issue is what you're doing with language and content that leads to the use of so many of them.
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.