If the azw3 looks bad on your Kindle, then the original format was probably as bad. Or you have changed something in the conversion settings.
The best way is to convert the epub directly to azw3 and leave the mobi out altogether. And you should take a look at your epubs in the Calibre viewer. If they look good, but the converted azw3 will look bad, then there's something in your conversion settings that messes up the result.
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