Countless hours of hackery later, I've managed to get a decent Java interface to Wordnet 2.0 working. I had to wrap around the existing library to spit out Java datastructures, instead of awkward classes. This was the last piece that I wanted. I am beginning to both like and hate different aspects of Java at the same time. Weird :)
Now I need to put all of this into an application and demonstrate it to my supervisor. Here's hoping I get a thumbs up or at least a mild "ok, carry on".