Flapping-wing flight is a challenging system integration problem for designers due to tight coupling between propulsion and flexible wing subsystems with variable kinematics. High fidelity models that capture all the subsystem interactions are computationally expensive and too complex for design space exploration and optimization studies. A combination of simplified modeling and validation with experimental data offers a more tractable approach to system design and integration, which maintains acceptable accuracy. However, experimental data on flapping-wing aerial vehicles which are collected in a static laboratory test or a wind tunnel test are limited because of the rigid mounting of the vehicle, which alters the natural body response to flapping forces generated. In this study, a flapping-wing aerial vehicle is instrumented to provide in-flight data collection that is unhindered by rigid mounting strategies. The sensor suite includes measurements of attitude, heading, altitude, airspeed, position, wing angle, and voltage and current supplied to the drive motors. This in-flight data are used to setup a modified strip theory aerodynamic model with physically realistic flight conditions. A coupled model that predicts wing motions is then constructed by combining the aerodynamic model with a model of flexible wing twist dynamics and enforcing motor torque and speed bandwidth constraints. Finally, the results of experimental testing are compared to the coupled modeling framework to establish the effectiveness of the proposed approach for improving predictive accuracy by reducing errors in wing motion specification.