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Yeah, I'm working on a book from archive.org that was OCR'd from a pdf and they can be ugly. So far mine isn't so bad.
Maybe look for the errant spaces using search and replace?
If I were doing it I'd fix the chapter names in the body of the book, then make the toc match them exactly. I don't know what calibre's editor does but I'm using sigil and it can generate an html toc for you using the content of the h? tags.
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