Reading a novel through from start to finish gives you one perspective. For different angles, leapfrog through the manuscript, selectively reading related passages. This will help you tease apart more of the issues that need to be addressed so you can better focus your revision. Your scene-by-scene outline provides a useful guide for selecting scenes to reread, each time through.
Here are some ways to select sections to reread, and questions to ask yourself as you do so:
By subplot: Leapfrog through the manuscript, reading each scene that develops one subplot, then jump through reading the scenes that develop another subplot until you've read them all. Ask yourself: Does each subplot have a beginning, middle, and end; if any are unresolved, is that a deliberate choice; is each subplot essential to your novel?
By character: Read every scene that contains one of the characters (not the protagonist); then read all the scenes that contain another character until you've run out of major and supporting characters. Ask yourself: Is each character sufficiently introduced and developed; does each have a distinctive and consistent look and feel and voice; does each act as if what's happened in the novel has really affected them physically and/or emotionally; are any of them stereotypes; have you shown how the character changes (or doesn't change); could the character be eliminated without damaging the novel (in which case, consider deleting him from the story)?
By setting: Read each scene that takes place in each particular setting until you've reviewed all the settings. Ask yourself: Has each setting been sufficiently introduced and established; is each setting consistent each time it is reprised, and are the added details consistent; did you establish the elements of each setting that are important to your plot?
Read It Aloud
Reading your manuscript aloud to yourself is time consuming, but provides unique insights. Hearing the sentences you've written exposes all kinds of problems. Awkward phrases, clichés, repetitions, and passages that go on for too long are readily recognized when you hear them read aloud. Clumsy sentences that you might have glided right past jump out when you hear them.
Pay attention to your own response as you read. If you get bored reading the story, you can bet your readers will, too. So make a note of places where you want to cut or trim and tighten, or perhaps insert conflict or action to make it more engrossing.
Reading your manuscript aloud to yourself will also keep you from doing what all of us tend to do when we get tired — speed up and skip ahead.