Now that the project is long finished and my marks for the year have been given I thought I would share the final report for the project.
Although the project was not completed, with me unable to finish tuning the PID control loops to a standard were it would be able to fly, I was successfully able to get the quad rotor to be able to balance most of the time on its test jig. Hopefully at some point in the future I will be able to finish the project, but at the moment there is just too much to do and not enough time.