What you need is a format that allows embedded fonts, and a publically available font that supports Khmer. One good option is ePub, but it is not available on the Kindle.
Unfortunately, Kindle's AZW (MOBI) format does not support embedded fonts. So if you want something that works on a Kindle the best option is a PDF with embedded fonts that has a page size optimized for a small screen. Most PDFs don't work well on the Kindle because thay assume a letter/A4 sized page. Since you are creating your own PDF from a word processor (say), you can optimize the PDF either by changing the page size or by using a big font size. All that matters is how many words fit on a line (you want fewer words on a small screen).
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