This doesn’t sound silly at all - in fact, it’s one of the basic problems in research method. I’ve faced this problem regularly in my own research – and I’m not confronted with a defense deadline 
Take a look at this thread and its scripts - as well as the threads internally referenced there. The scripts in that thread operate on a RTF file – you can convert OCRd PDFs to RTF in order to use the script. I’ve noticed you’ve cross-posted your inquiry to the Tinderbox forum. I wrote the scripts in the above thread because I then take the exploded notes and dump them into Tinderbox, where it is easy to create note attributes, agents, and maps that can help your research and evaluation of the written texts. Lots of advice available in that forum too.
Look also in the scripting forum at the variety of annotation scripts. Try also the annotation script that’s packaged with DEVONthink.
I advise experimenting on a small subset of your library; get a technique, then stick with it.
If you have some time, listen to David Sparks’ Mac Power User’s 100th show (posted today) which has several interesting segments on research – including coverage of DEVONthink and Tinderbox.