hmmm, how about saving the PDF as a Word Document (if you have the professional Adobe rather than the Reader) and form there on it's as simple as finding the specific text of the header/footer (a nice CTRL+F and copy pasting the text) and then replacing all with nothing so they'll poof... disappear
[if you only have the reader, i think you have the option to save as TXT, from where you'll have to copy-paste into a Word.]
from there it's easy to save as HTML and do what you want with it (use calibre or mobipocket creator <--- i'm really liking this one, moves lighting fast to convert to .prc--accepted by kindle--and it keeps your formatting specs)
i hope this helps even thought it sounds a bit complicated
you wouldn't happen to have Open Office installed, would you?