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Your second issue is just simply a preference setting in the Kobo. In Reading settings, remove the check mark next to "Show Adobe EPUB page numbers:"
Your first problem with the margins is a bit more difficult. By default output setting, Calibre overwrites page margins in book and replaces them with a default set of 5pts. (You can verify that's still the case for those books, in case you had changed the margin settings in a previous coversion. When you convert the book, click on the "Page Setup" option on left side, and confirm that the margins are all still 5pt.)
If the problem is not in the page setup option, then there is some unusual styling code in the book that will have to be manually cleaned up. You can install a "ScrambleEbook" plugin in calibre that will let you create a special version of the book with the text scrambled, which you can post here for help.
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