In my experience, it is best to use the native format for your Reader. For pdf conversion to LRF BookDesigner is the best choice in my opinion.
For PDF reformat, in another thread someone posted a nice conversion method:
1. Export to DOC (I am not sure what is the best tool for this, Adobe Acrobat Pro is very poor, Abby Finereader is better, but very slow).
2. Change page size in MS Word or OpenOffice to your Reader's spec
3. If needed resize and copy pictures from the original PDF.
4. Convert to PDF (OpenOffice does this for free, or look for PDF printer software)