PDF stands for (P)ortable (D)ocument (F)ormat. I'm not going to conmment one way or the other on the merit or advisability of using PDFs to secure material. The primary point of PDF was to be able to create portable documents (multi-platform) with scalable graphics and fonts (i.e, no bit-map images, unless you're a complete hack).

There are a number of third party Windows based tools for manipulating PDF files, so I'll assume there's not an issue about securing the content, by default. I believe that 4.0 supports some security features. You can turn off the ability to cut and paste (at least, out of the Windows viewers. Dunno about other platforms).

There are, in fact, some tools that do create searchable indexes for PDFs. All the ones I've seen are Windows based, so I can't comment if there are any with source available. I think some third part vendor out there offers a linkable library for PDF management.

I realize these don't directly address the answer you're looking for, but may give you some places to take a look for additional information.

--Chris