ePub won't work on a Kindle. You can however, save as ePub, then convert to Mobipocket format, which usually works fine, once you get the ePub version fixed up.
I don't have Adobe software other than the reader, so I don't know what options you have. The page numbers, titles, etc. are just text converted from the file. If there is some way to extract the information from the original PDF file without all that, I'd do that, then convert from the extracted text.
You might want to try Mobipocket Creator, Publisher edition (also free, like Calibre). Sometimes its conversion of PDF is better than Calibre's. Also try the Amazon conversion service (email the PDF as an attachment to one of your Kindle addresses, with "convert" in the subject line).
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