I understand your university's position ... and yours also. If they do decide to make the code publicly available, I'd appreciate a reply to this comment. I'll check back occasionally to look for updates.
Enjoying you're thesis, btw, especially the section on Bollinger bands. The Turtle Traders (http://bit.ly/by1j2M ) seemed to have used this successfully with commodities. Did you reference any of the Turtle traders stuff when you were designing your system?