A trick I use if I am not happy with the mobi to epub conversion in Calibre is to add a middle step. I convert from mobi to txt then quickly check out the txt file (within Calibre) and then format from txt to epub. This even adds a TOC sometimes when the mobi to epub doesn't. As the txt reside in the same folder as the mobi file the book cover is usually added to the epub file automatically.
John
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