This is too big a question to explain pithily, Andrew, but I will say that your 1000-word rule is wrong. That's a whole lot of words, for one thing. For another, a lot depends on which words of a book you quote. There's a famous case in which the Nation magazine used just 300 words from Gerald Ford's then upcoming memoirs, and it was ruled not to be fair use since those 300 words were key to the book -- they had to do with his pardon of Richard Nixon.
Fair use is almost always a judgment call. No computer can tell you if your use is fair. It involves a weighing of factors. So the only way to achieve certainty is to ask for and receive permission. If we were talking about posting something online, then you could give yourself the benefit of the doubt and use whatever you think is fair, since it's easy enough to take it down if a problem arises. But when you are publishing an old-fashioned book with binding and paper, I think you need a higher level of confidence that your judgment is correct. Most big publishers are very conservative when it comes to such matters and insist that their authors obtain permission for just about everything, even if a strong case for fair use could be made.
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