Along the same lines as Daniel suggests, have you tried simply using the File --> Print method of creating a PDF of your PPT deck? This method completely bypasses using the Adobe Presenter Publishing methods, but it still offers you the ability to incorporate the notes from PPT without having to deal with the media aspects (audio, etc) when PowerPoint prints the deck to your printer driver.
The only major drawback is that I've seen the notes content getting clipped in the PDF versions of a PPT deck; this is due to the limitation of the output from the printer driver (typically set to 8.5 x 11 in portrait mode). So the more content in notes, the more likely that it'll get cut off at a max character count.
Nevertheless, once you print a PDF version of your content, you can easily add the new doc using the attachments feature that Daniel recommended above.