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If you haven't used Sigil before there are a couple of things you should know...
(1) the Open With plugin is darned handy to use to be able to launch Sigil directly from calibre (particularly with a keyboard shortcut).
(2) the currently released Sigil 0.5.3 is horribly crash-prone (on Windows at least) particularly for the actions you want to do. For instance do *not* do this sequence:
1. Open ePub
2. Double click on the html cover page you think you will be removing
3. Switch to code view (such as to see the image name)
4. Right-click on that html page in the book explorer and choose "Remove".
I would suggest using an older more stable version (such as 0.4.2), or else do any remove operations before you do any actions that involve switching to code view (like as mentioned above or opening a stylesheet).
You should of course also remove the associated cover image for an inner cover or else it will be orphaned. You can either do that in Sigil, or just delete the html page and then run Modify ePub with "Remove unused image files" afterwards.
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