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Regarding your cover problem. I think Calibre's default is now to stretch the cover to fill the screen. If you look at the Convert|EPUB Output page there is a 'No SVG cover' option. If you check this box I think you will get back to what you want. If it works for you then you can set it permanently in Preferences|Conversion|EPUB Output.
Regarding TOC. If you're trying to specify <h1> tags in 'Convert|Structure Detection|Detect chapters at' and/or 'Convert|Table of Contents|Level 1 TOC' then the XPath entry should be //h:h1 Is this what you used? I find it easier to use the magic wand wizard button alongside these boxes to construct the correct XPath.
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