see my other reply to you about the mobipocket creator software. i have not tried the PDF import myself, but i've read from some other folks that it seems to work fairly well (depending on the source file), and certainly better than DTP is doing thus far.
PDF is a bad format for conversion to a reflowable text edition such as Kindle. If you have the original source files that you saved as PDF (e.g. Quark, InDesign, PageMaker, Word, etc), please try to save/export your content as HTML instead.
However, when I went to export into HTML from my master QuarkXPress 7.3 file, I ended up with a series of html files, one file for each page, and Amazon wants a single file uploaded. So, that's a no-go.
Frankly, I'm thinking this DTP system is bunk. Why can't I just sell my copy-protected PDF file on Amazon as I did before they converted to the useless DTP system?
Amazon is losing thousands or millions or dollars in sales revenue because their PDF conversion system is crapolicious.
the first thing i'd try would be to upload the file in its Word format (it has to be .doc, i believe; if you have a later version of Word that produces .docx files, just "save as" an earlier version of Word).
upload that, then check it out in the preview tool. if it looks okay and the pics are where they're supposed to be, you're likely in good shape.
if not, my next suggestion would be to save your file in rich text format (.RTF), then try uploading that.
It is pretty easy to format a 'Kindle-specific' designed Word document and convert it to PDF. If I can then email that to my own Kindle and have it render in a wonderful format, wouldn't it seem logical to allow us to upload the PDF WITHOUT taking it through the DTP reformating process that gums it up?