Have you tried ScanTailor? It is free and open source. I have a mac so I use ScanTailor via Crossover. Though if you have macports installed then ScanTailor is easy to install. Unfortunately Homebrew does not have a cask for it yet.
http://scantailor.org/
It is designed as a preprocessing tool so it works on batches of scanned images. If you already have a pdf then simply export the pages as images and enter them into ScanTailor. Then use the various settings to crop the headers and page numbers, deskew, set margins etc . It will output in Tif format.
There is no easy one click method that I have found to batch crop out extraneous material from scanned images,