You have two options - follow Kovid's advice, which requires you setting up your css in pages to put spacing between paragraphs using margin-top and margin-bottom styles that spaces things out like you want them.
The other option would be to go into the 'look and feel' options in Calibre and select the option 'remove paragraph spacing'. This will leave your blank paragraphs there, but change all the paragraphs so they have a top/bottom margin of zero. Note that setting may also modify your paragraph indents.
Last option would be to use Sigil to add a cover into the file manually.
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