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In order to change the Adobe PDFs you will need to strip their DRM. Even if you do this, there is currently no automatic tool that will reliably convert them to ePubs (or any reflowable format) although several tools might work in some cases.
As AnemicOak says, if you are going to strip DRM then strip it from a reflowable format. The best for conversion to ePub are, 1) LIT, 2) MOBI, 3) eReader. Each one requires its own DRM stripping tool, but, once DRM-free, Calibre can convert them all to ePub. LITs are only easily handled if you have a Windows PC, but are very close to ePub in structure. MOBI works well enough converted to ePub, and is more often available than LIT. The eReader format is designed for small screens, and typically has less structure than the other formats but it is reflowable and probably better overall than PDF unless the ebook has many illustrations.
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