PDF isn't viable for converting. To get a good PDF "conversion" you'll need to OCR the PDF and then convert the text.
I'd say it depends mostly on the PDF in question. If it's all text anyway, you can probably do fine. There are also programs that convert PDF to something like a Word file. If you're having trouble with formatting, try doing that first, formatting the word doc the way you want (or make it a text doc) and then convert to Mobi. You might get a better result.
A PDF with lots of embedded images, charts, etc. or odd formatting like columns and things that cross them will NOT convert well.