— This paper builds on previous work on optimal methodologies for the design of numerical subsystems for non-linear, uncertain hardware-in-the-loop (HWIL) simulators. Firstly, three important extensions to the existing methods are presented: the limitation to SISO systems is removed, allowing full MIMO design; a method for the design of an important and previously neglected component of the numerical system is described; and finally measurement noise and other unstructured uncertainty is tackled more rigorously and explicitly than previously. Secondly, as a case study the extended method is used to design a numerical system for a real HWIL simulator, and the results are shown to outperform those produced using classical design methods. The system used in the case study is a high-performance simulator for small aerodynamic objects that is in the final stages of development.