Adobe Acrobat Pro or Nitro PDF or PDF XChange Viwer Pro have a usefull crop function to remove the white border in PDF. That way the eink screen is better utelized and it needs less zooming while reading. For PDFs with mainly text you can try OCR e.g. with Adobe Acrobat Pro, eventually remove images and charts with Nitro PDF. A text based PDF can then be converted to EPUB with Calibre.

The free version of PDF XChange allows PDF annotation.