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A agree with davidfor that the ebook-convert command line tool is your best option. Note that I have seen the FBReader centering bug in about 1 in 10 conversions from MOBI to ePub (I have not tried PDF -> MOBI -> ePub). I only use FBReader to check the resulting ePub for obvious problems, so the bug is not an issue for me - but the FBReader team really should fix the bug and I don't know if it has been reported to them.
If you have the author and title in the filename, then you could alternatively try the GUI by setting Preferences -> Add books -> Regular expression (and unchecking Read metadata from file contents) and then setting an inverse Save template for Sending books to device.
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