First make an epub and then use that with kindlegen instead of a html.
If I may say so, you seem to be overly obsessed of how your book looks exactly. You will never achieve perfection in a reflowing format. Just change the font-size and everything changes. If you want that type of control, you need to make a fixed format book. But: That is much more complicated. And you will alienate most of your possible readers, by taking away their ability to customize the look of the book. People reading eBooks know and live with the limitations. People who can't stand this read paper books. Maybe sometime in the future we will have better renders.
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