I finished with the new Board class. The biggest difference is the way the piece lists are handled. In the old version I had a class called Piecelist with some very dodgy methods. This is now replaced with a two-dimensional array (12x10) where all the pieces are stored.
I'm running a new tournament to try it out at the moment. It seems it is doing quite well with a slightly faster move generation.
However the biggest bonus is the much clearer code in the Board class.
I don't think this change merits a new release on it's own so I will wait with releasing it until I've made some progress in other areas as well. However if you're interested the changes are commited to the repository on Sourceforge.