To this day, the best tool i have found to convert documents to kindle format and upload them to the device is Calibre (http://calibre-ebook.com/), besides is a java software so it doesn't matter what operating system you have.
The most difficult case, a PDF document which have line breaks, headers, footers, lets see how its done:
1) Open calibre and add your source document (pdf in this case) using drag and drop
2) Select the file (title) and then click Menu > Convert Books > Convert Individually
3) At the Heuristic Processing section choose "Enable heuristic processing" in order to remove the line breaks from the original document
4) At the Search & Replace section add the replacements for the header/footer texts the book has, beside it is possible to use regular expressions for advanced users, if not, just write the undesirable text
5) Finally hit Ok
To upload the book to your kindle:
1) Connect your kindle using USB cable
2) Select the file (title) and then click Menu > Send to Device > Send to main memory
It's pretty straightforward
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