This work explores a paradigm in which isolated aircraft components are analyzed separately and combined together in a multi-body system representative of the whole geometry. The FLAPERON (FLight mechanics Analysis and PERformance OptimizatioN) toolbox is developed and employed to assess the impact of vortex-filament-based aerodynamic interactions on the simulated aircraft's response when considering aerodynamic data only at the component level. Physical networks created in Simscape are used to simulate symmetrical flight and assess key stability characteristics of a configuration including a main wing, a horizontal stabilizer, and a vertical stabilizer. Vortex filaments are modeled for the main wing and the horizontal stabilizer. The introduced aerodynamic interactions change the simulated response of the aircraft in accordance with predictions. This work suggests that multi-body analysis of flying qualities is possible based on the data prescribed at the component level.