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Sounds like you probably have everything.
When you say you are backing up 'my books' I assume you mean the folder and everything within it (which includes the metadata.db file) - if so, that is everything in your calibre library. The files under your User are all the calibre preferences for that user.
As you correctly surmised, you do not need to back up the binaries - these can always be re-instated by simply re-installing calibre.
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