When I'm writing or revising, I try and pay attention to the shape of the story--the plot and characterization arcs, the pacing, how the subplots feed in to the main plot, and all the myriad other details that make up the whole. When I finish a project, I let it rest overnight and then read the whole thing in one sitting if I can. That gives me a good idea of the shape of the book and tells me where I need to make immediate fixes. Then, once I've done the initial revisions to take the book from a rough draft to a first draft, I set it aside for at least a few months.
During those months, without really consciously thinking about it, I get a real sense of the story. And when I come back to it, I already have a good sense of where I need to rewrite to pick up the action or the pacing, what I need to cut or add. But first, I reread the whole thing. Then I make the changes. If I make drastic changes, I'll reread it again afterwards to make sure I haven't wrecked the flow or left out details. Then I'll set it aside for a while longer and see if it still seems okay when I reread it again.
I read my own stuff countless times. The more problems a book has, the more I read it, work on it, read it again. The best thing about so many rereadings is that after a while, I notice myself skimming some parts as boring. And then, those parts must go. Boring to me = boring x 1 billion to readers, who don't have all the energy invested into the book that I do.