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I use the Calibre plugin "Modify epub" to do most of the things you're looking for and there's a few other Calibre plugins that do this as well. It uses the Calibre conversion templates without actually converting and gives a good first bulk edit.
But it doesn't discriminate in applying the templates and can cause trouble eg applying a paragraph text-indent adds it to all and can cause drop capitals in leading paragraphs to be oddly placed. I usually underprescribe with the plugin and use the Calibre editor on individual books to finish.
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