One of the challenges for manned-unmanned air vehicles flying in joint airspace is the need to develop customized but scalable algorithms and hardware that will allow safe and efficient operations. In this work, we present the design of a bus-backboned UAV microavionics system and the hardware-in-the-loop integration of this unit within a joint flight network simulator. The microavionics system is structured around the Controller Area Network and Ethernet bus data backbone. The system is designed to be cross-compatible across our experimental mini-helicopters, aircrafts and ground vehicles, and it is tailored to allow autonomous navigation and control for a variety of different research test cases. The expandable architecture allows not only scalability, but also flexibility to test manned-unmanned fleet cooperative algorithm designs at both hardware and software layer deployed on bus integrated flight management computers. The flight simulator is used for joint simulation of virtual manned and unmanned vehicles within a common airspace. This allows extensive hardware-in-the-loop testing capability of customized devices and algorithms in realistic test cases that require manned and unmanned vehicle coordinated flight trajectory planning.