For PDF's that don't render well try this free Mobipocket Creator:
I had PDF's that were manuals with tables also (two columns on the page).
I converted tp PRC and they remder much better. It is not perfect but for non-standard docs, it works well.
I think there is also software out there to convert to WOLF format (which is XML-based I believe). Haven't tried that yet, but you may want to give it a try.