Undisciplined cohesion and coupling undermine countless aspects of quality software. Students, however, unfortunately tend to gravitate toward such approaches. This system mitigates this problem by forcing them to communicate with their components through a well-constrained hierarchical virtual network of networks. The application is a dynamic, plug-and-play aircraft fly-by-wire system that processes a wide variety of commands to design, construct, and manipulate sensors, actuators, controllers, and communication buses concurrently in a flexible model-view-controller architecture. It successfully employs many systems-engineering concepts of modeling, simulation, visualization, and analysis toward the goal of instilling disciplined design, implementation, testing, and evaluation practices in students. In particular, it provides the pedagogical and programmatic frameworks for creating, executing, presenting, and analyzing meaningful test cases as part of formal test plans carried out in controlled experiments via scientific method. The system can be adapted relatively easily to countless other real-world multidisciplinary domains for reuse in other projects. Extensive results from classroom deployments show that students overwhelmingly benefit from this approach.