Eg I notice that some of my epubs (converted from pdf) have (pointlessly and annoyingly) inserted the title of the book every few pages of text!
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that is a problem of conversion from pdf ; those are actually the page headers, which sometimes get translated as part of the text. i agree, incredibly annoying. if they are all the same though, they are easy to get rid of with a simple search (for header text) and replace (with nothing). page numbers are usually trickier, but you can automate those too particularly if there is a footer text (that makes it easier to find them).
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This search and replace operation of which you speak - do you do this in the pdf (opening it presumably with Adobe) before loading it into Calibre? (no option to do it within Calibre that I can see..