hi... i used to have the same problem with pdf files ... im not expert but i think the only way to remove those are with either a software to convert pdf to word and then remove the header& footer manually or to use a regular expression i think, anyway i found long time ago a program that converts files to pdb files (palm ebooks) and it does it on 3 steps first it converts the pdf file to txt, then cleans the txt (the result may be wrong but almost every time deletes header & footer) and then converts this clean txt file to pdb, but you can use the clean txt file and import it to calibre (it what i do) so... it maybe suit you... hope i make myself clear cause my english ... not very good... anyway here's the link
http://www.reblusoft.com/index.php?o...d=20&Itemid=49