You know I had actually considered this exact thing you want a while back as a way to move forward once I had the program working. You could design all the graphs, logical connections on the computer then load them and just snap all the parts together. The main drawback I encountered then was how to implement the wagon since it can move in an arbitrary track path circuit. I'm not sure how that could be done. Another idea that's a little out there is that if someone could implement the basic building blocks using molecular parts, then maybe that's how we build molecular machines!