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The page numbers on the right aren't a feature of the Story, James. They're generated by the Adobe Digital Editions software, which the Story (and many other readers) use to display ePubs on-screen.
There are many complaints about them on the Adobe forums, with many other people being strongly in favour of them. But they can't be disabled. About the only thing you can do is as Greenapple suggests -- widen the right-hand margin so the numbers don't overlap the text.
If it were me, I'd probably do it in Sigil, but that's my personal preference. I find Calibre a bit problematic, and also that it can sometimes lead to unexpected and unwanted outcomes in formatting when it takes it upon itself to adjust what it sees as mistakes.
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