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I would just generate a PDF. Then you can use all the fancy formatting, math symbols, etc. that you like. KT supports PDF links and bookmarks (for TOC), TTS, and notes/highlights. You get to see exactly what it will look like as you edit the source document.
For the best WYSIWYG make sure to set the page size (in Word or whatever) to something like the Kindle screen size, set margins to zero, etc. so you make the most of the small screen.
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