I don't read PDF books. The PDFs I prefer to put on my Kindle (99%), are those I've made myself. I make them with MS Word and make the page size the dimensions of the screen with a larger font. Then I use CutePDF to print to PDF.
If it's a document with links, I use the CutePDF software to add them in after the PDF is created. There may be software better suited for this but this is software I use for work and am more familiar with.