I took the Computer Security and Internet Security courses from Professor Du at Syracuse University, years ago. Both courses had end projects that required extending a kernel and userspace to implement security functionality.
At that time, we had the option to work with MINIX. Here are the MINIX Role-based Access Control and Firewall Labs:
Professor Du's materials are also packaged for self-learners and other teachers to use, as the open source SEED project. A few of the current SEED projects are implementation-exercises similar to the above two labs.