I don't know about calibre, but once you make the changes to your html file and your opf file, you should then convert the
opf file with kindlegen/previewer. What you've described is what happens when you try to convert the
html file (which knows nothing about the opf file). All files must remain in their relative position to each other in the directory structure when feeding the opf file to kindlegen, too.
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It seems as though some of the requisite CSS is missing -- there are no stylesheet settings for paragraphs in the HTML anywhere in the html file, just the inline formatting on the tags themselves (which doesn't specify margins or indents).
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That's mobi markup. There is no css--inline or otherwise. It's basically HTML3. Left margins are done with <blockquote> and indents are done with the "width" parameter of the <p> tag. Top-margin is achieved with the "height" parameter. There are no right margins or bottom margins in mobi.
Also, when using kindlegen, you need to make sure you're viewing the mobi part of the conversion and not the KF8 part (which will also look exactly as you described if you fed the converter mobi-only source code).
You can also use KindleUnpack to split the mobi-only portion of the resulting file from the KF8 portion.
The bottom-line is (and I know this is probably confusing): mobi-only source (html) is not suitable for building KF8 kindlebooks.