It sounds like a fairly big task in itself.. I thought a bit about it and perhaps you could try one of the following approaches...

Firstly, if you need full text searching, its probably wise to build indexes first... searching all the PDF files on your server is going to take far too long, and you could run into scalability and concurrency issues..

So the solution would probably be to periodically convert the textual content of the PDF files into a text file, and index that text file... Text indexing is pretty well understood, and its fast, moreover, so this would probably be the most efficient method.. Just provide a link to the real PDF file in your search results

Another thing you could try is to convert the PDF to HTML (see the links below).. Have a converter program product HTML output, and then run an indexing tool like ht://Dig or something on the HTML output.. Then, your users can read the output in HTML, and if desired download the PDF format document.

These are some links I found that might make your life easier, mostly to do with PDF conversion from one form or another, but there are some links on how to convert PDF to other formats as well...
PDF tools
Perl modules for PDF conversion
HTH