A pitch for the freebies: have you tried
pdfreflow, or
calibre, or
Abiword?
No don’t expect perfection from any of these. PDF was meant as an output format, not an input format, and hence doesn’t contain the necessary semantic mark-up, and so all these conversions rely on somewhat imperfect algorithms for “guessing” document structure based on layout, which is not easy to do.
They can all do batch jobs, since they can all do their work from the commandline. Probably best to settle on a tool before getting into details about batch conversions, however.
I stand by my belief that PDF is still the best ebook format there is; it’s just not the best for distribution.