Hi Ben,
I'm not really sure of a good strategy for indexing pdf documents directly, most solutions I've seen require some external indexing server. One of my customers had the same need and what I did was add a description field to the shared files feature, so what they do is copy the text content from the pdf and paste it into the description as plain text so it can be indexed by our search engine. They keep the description hidden and use it only for this purpose to make their pdf files come up in search results.
Hope it helps,
Joe