PDF is a valid route, but remember if you're planning to publish pdf for the Kindle you need to publish to the Kindle's physical pages size, otherwise any attempts to actually read the document would be worse than a poor mobi conversion. You'll probably want one pdf for the regular Kindle and another for the DX.
Several fixes are now going into the next release based on this thread which will improve mobi conversion somewhat, but I think most of your concerns relate to inherent issues with the mobi format itself, and less with Calibre's conversion.
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