As someone who feels a rework would do wonders for certain parts of the game, I agree that this is likely the best approach for you to take. With each chapter you are building the skeleton of the game, and before you have it complete, or very near complete, it may be hard to judge where it needs "more muscle" or where it needs "some fat trimmed". Once the skeleton of the game is complete or near complete, you will be able to make those calls easier, since you will know what was the journey each character took through the story, and the journey the story itself told; a better idea of the whole body you created. Knowing that, it'll be easier to identiy what parts need to be adjusted to be more in line to those narrative threads, what needs to be removed because it's too in conflict with them, etc.