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Forget mobi except as a last resort. I always use azw3. I don't worry about hyphenation but if I did I would use Hyphenate This! or similar. KFX gives enhanced typesetting but is a very poor format for archiving and conversion, though this probably won't be a concern with your current books in epub. Using another Calibre plugin you can actually unpack an epub from an Amazon azw3 file (without drm of course) without needing to convert.
Try both, see which one you prefer.
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