I just use Sigil. If the source epub is really bad, I might run a conversion in calibre. That can sometime clean it up and make it easier to fix. But, usually I just use Sigil and lots of regex. And I'm using Sigil rather than the calibre editor mainly out of habit. The calibre editor is handy as it doesn't fiddle with the code when it opens.
I do have epubcheck, but I only use it when I am debugging a problem like this. That usually means someone sent me a book that wasn't working and I did the check before fiddling with the file.
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