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?
Very interesting. Did you consider using R? Why did you choose Clojure for this? I've been thinking of doing something similar myself and I would love to hear your thoughts considering you've already been-there-done-that.
I'd love to read your thesis and code, if they're available.