Since you're asking about the .mobi format, I'll assume you want to create an ebook compatible with Kindle. Putting a PDF into .mobi format is going to be an ugly result. You are best to start over and generate fresh HTML, and feed that to Mobipocket creator. But if it's true, and you want to put this on the Kindle, keep in mind, the Kindle can read PDFs without modification. However, on a Kindle 2's small screen, and the fact that PDFs will not allow resizing text, you should keep your fonts at 16 point or higher, or it will be unreadable.
I work with every e-book format that's popular. To best answer this question, it would help to know what you are hoping to achieve. More specifics would help.