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I'd suggest doing it manually, too.
You can find the capitals by doing a regex search for "[A-Z][A-Z]"; that will find any two consecutive capital letters. This kind of thing is a pretty standard part of converting PG texts. It's complicated by the fact that some of the words in capitals should probably remain capitals; the only way you'll find that is when you carry out the next stage of your eBook conversion - a thorough proof-read against a page scan or printed edition.
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