I had the same problem once. Every end of line had a paragraph return on it when exporting to RTF or DOC. The only way I found to not have the end of paragraphs all over the place was to export the PDF to HTML with CSS from Adobe Acrobat Pro. Opened it up in the browser and copied it from the browser back to the program I was using to edit it.
There was an option to not export headers and page numbers. Though a few crept in.
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