The number one error I see in manuscripts, and I've evaluated hundreds, is that writers often don't do what they think they want to do with a story, and this is evident when I compare a synopsis to an actual story. They often don't match. The synopsis is typically plotted fairly well because it's easy to capture an idea in a few pages, not so much in a few hundred pages and that's where a writer's idea and a writer's execution of that idea part ways, and often, 'never the twain shall meet.'
The best way to ensure that you’ve covered everything that’s supposed to be in your story (according to you), and to determine if your story flows well, has proper pacing, good plot points (and actually to determine if it has any at all – I’ve seen plotless stories before) is to do the following. It will take a few hours, but the information you get from this exercise is priceless.
1. Print a copy of your manuscript. Yes, print it.
2. Set aside a few hours and go somewhere quiet, like the library.
3. Make sure you have paper and pens.
4. Now the fun begins. Write down chapter 1. Jot down characters and events, and anything else that is relevant, whether it be dialogue or setting. Basically sum up what happens in the chapter. Point form, no complete sentences.
5. Do step 4 for the entire manuscript.
Something else I like to do as I do the above, is to jot down any questions that come up, gaps in plot, or anything else I notice that isn’t working. Also make up a list of characters. It might reveal some things. Even better is to prepare character sketches by listing key things characters say and do, what they look like, and any mannerisms you’ve given them. Having this list will help you see your characters better.
Once you’ve broken down your story, review it. Do things flow as you had hoped? Is there an actual story there? Is it the story you want? Have you forgotten key events? Are your characters believable? Are some characters too similar? Are others not necessary? If you’re honest with yourself, you’ll find the exercise will be an invaluable tool in your effort at rewriting a story that is tighter and tells the story you want.