I know, probably been beaten to death

, but I'm still pretty new here and while a competent end user, I'm not a real expert on file formats and such.
I'm hoping to move PDFs that have two-column pages over to ePub and actually get the text formatted sanely in the process. At this point, I'm leaning toward extracting the text from said files, then running the result (after manual cleanup) through Calibre to ePub (I've tried direct conversion with disappointing results), but have yet to figure out what's going to be my best intermediate format to get decent output that'll be readable on my iTouch.