The specification for PDF files is available as a freely downloadable PDF from Adobe - or at least it was last time I checked. However, most PDF files have most compressible data in them compressed. There probably was a basically plaintext version of PDF once upon a time, and if so it will still be valid now, but actually getting a file in that form may be a problem.
Although I haven't done it, one very likely possibility (if you're willing to pay) is to buy Acrobat Pro, and to use the Javascript scripting abilities built into that application. To get you started...
http://acrobatusers.com/tutorials/2008/10/auto_bookmark_creation
This tutorial shows how to create bookmarks automatically using Javascript in Acrobat 7.0 Pro (the version included in Creative Suite CS2). Although that's getting a bit old, the same technique should work fine for newer versions.
Adobe applications do include a library for reading/writing text files using Javascript (something that Javascript doesn't have as standard), so it's possible to write your own import/export scripts, though non-trivial to make those scripts robust.