Both of the tools I have found for creating Sony LRF ebooks assume a left to right reading format. Therefore, the way I would make them would be to set up the word processor using either an OpenType, TrueType or ATM Type 1 Farsi font and output the to Adobe Acrobat scaled for the Sony Reader with embedded fonts.
Once you have a PDF scaled for the Reader there is no reason to change it to anything else.
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