Most cartography for publication done using electronic files was done using FreeHand to post-process for publication raw files exported from Geographic Information Systems (GIS) --- since Adobe bought them out, most map makers have grudgingly begun switching to Adobe Illustrator.
You should be able to achieve what you want by placing the .pdf into a program such as InDesign or Scribus or Illustrator or Inkscape and adding the customizing elements over it.