Extracting Excerpts From My Own Wiki Articles - Looking For Suggestion

Hey All, I've been working on some internal software for the company I work for. It's kind of an extranet based work assistant that works along side our corporate business package. One of the functions is when certain selections are made within the software I am pulling excerpts from a private roadkill wiki engine we are using for things like internal policies, HR and different kinds of guides(I don't write or publish the articles so I have no control over formatting). The full wiki is read by new employees and then just reminder excerpts are used after that. When the selections are made there may be references to several different wiki articles and different sections within the article itself. I need to be able to work with and manipulate the content coming from the wiki.
I've tried a few different approaches:
First I worked on extracting the articles using sql direct from the wiki database. Easy enough, but it's markup is Creole and work ...