I don't know how comfortable you are writing your own, but pdf saves the components with coordinates, bounding box etc so you should be able to automate it with a small script that reads pdf components directly.

Also try qpdf to convert pdf into qdf format, then you can open it in a text editor, find the element you want to remove. Look at examples of few pages, find the pattern and do regex replace. Make sure to keep a copy and check the diff before accepting it.