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I've pretty much given up on converting PDFs for my K3. In less time than it takes me to convert it, load it on my Kindle and see how well it works (which for me is 'not often'), I can crop the headers/footers/margins and read it directly.
I suspect cropping also can help out with conversion. One of the issues you can run into is failure of the conversion tool to ignore headers and footers, or failure of the PDF author to add tags to define the proper reading order, so you wind up with page numbers and headings inline with text, text out of sequence, etc.. Calibre has some sort of header/footer detection but it hasn't worked well for me and I've been too impatient to tweak it so as to work better on particular files. TOCs tend to get garbled as well. I'm no perfectionist, but it bugs me enough that I'd rather use the original PDF and deal with Kindle's PDF viewing limitations.
The K3's contrast adjustment is helpful in making small text more readable, and I can read most PDFs in portrait orientation. When that is still too small, landscape usually works well enough.
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