If you convert from EPUB to AZW3, the book will normally display perfectly on the Kindle.
However, if the EPUB is not justified, the AZW3 also won't be. You can set justification upon conversion, but I'm not a fan of that method. I normally open the book in the Calibre Viewer, and if it's not justified, I use Edit Book. Just find the the classes in the CSS that make up the body text, and add:
text-align: justify;
Or, if it's set to left, change it to justify. Save the book, and then convert it.
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