we are doing something similar with barcodes. we send out documents to be signed and they are returned via email/fax and we read the barcodes on the page to reassign them to the proper records

with PDF as long as it is a text PDF you can use any PDF library to get to the text. Then of course the tricky thing will be to find what you are looking for.
We use PDFSharp (of course not directly from DF but from C#)