@
soylent_bob - have you read this
Read this before Posting PDF Questions
As you'll read in there PDF is the worst format to convert from, sometimes what looks to be a simple looking PDF can be a pain to convert, and sometimes what looks to be fairly complex one can be fairly straightforward.
But in my experience very few PDFs will convert to something reasonable without some additional effort with an editor of some sort. For that reason its better to get the book into EPUB and convert that to MOBI as a final step.
And, you should also read this sticky
How to ask a question about conversion problems
FWIW My first choice is convert the PDF using the Mobipocket Creator tool to PRC and then - well it depends on what the PRC looks like. For me some PDF's are just too hard, eg I wouldn't even try to convert a car maintenance manual, that was full of images, drawings, often double column - too much effort.
BR