PDF is the worst file format for reading on eBook devices. However, you may try GoodReader or ReaddleDocs iPhone apps. They have a text reflow feature to extract and show only the text from the PDF file.
Also, you may try this tutorial about how to convert PDF to ePub on iPad. Results depend entirely on the PDFs that you want to convert.
Hope it can do you a favor.
Hey I would try to avoid using just the tool's alone if u know any programing u could do the extra programing required your self. If not then try a Manuel converter that way the files can matinee the correct formatting and wont look like gibberish.
You can convert pdf to epub on mac with the above suggested enosloft pdf to epub software. However if you are willing to migrate your iPad 2 files on your iPad or PC hard drive, in that case you are not supposed to use this software due its limitation. In order to perform file transfer, that time you are needed to use third party iPad 2 epub transfer software that safely transfers your files and all books saved with .epub extension on your iPad 2 or vise versa.
That's really unconvenient to read PDF on ebook device. So, i google a freeware 3dpageflip PDF to ePub Converter (from 3dpageflip.com) to convert PDF to epub and output mobile version(for ipad). It works fast and save my time. It is worth trying.