I'm going through a similar process with the final output being mobi (or plain text).
So far I've tested PDF conversions going straight to mobi with mobipocket reader or Calibre, or within Calibre with intermediate steps to RTF or txt.
Regardless of which method I use, the results are all over the place.
Sometimes mobipocket reader creates the best conversion. Sometimes Calibre makes a good conversion straight to mobi and sometimes the intermediate steps may (or may not) be helpful.
And sometimes none of the variations are very effective and I end up reading a very tiny pdf display on my Kindle 2.
I think my point is that none of the methods I've tried have yielded consistent results.
(My apologies in advance for sharing experiences with a non epub endpoint. I will say that Calibre routinely makes awesome conversions from epub to mobi.)
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