Second guesses

So, I finished the story on Saturday. It's now Wednesday and I'm starting to think I need to alter a few things in the book. Mainly, what motivates the hero and heroine on their journey. Right now I think its missing something. It feels flat. It didn't feel that way when I wrote it, of course, but now as I look over it, proofreading and revising, I see that it just doesn't jive for me.

Is that something anyone else experiences? Is it best to leave it be and just let it alone instead of playing Dr. Frankenstein with it; patching here, amputating there, and giving it a new brain?