There is currently a large effort underway to understand the physics of avian-based flapping wing vehicles, or ornithopters. There is a need for small aerial robots to conduct a variety of civilian and military mission scenarios. Efforts to model the flight physics of these vehicles have been complicated by a number of factors, including nonlinear elastic effects, multi-body characteristics, unsteady aerodynamics, and the strong coupling between fluid and structural dynamics. Experimental validation capabilities are crucial in order to achieve accurate simulation. A multi-disciplinary analysis methodology requires the evaluation of tools representing individual disciplines before they can be combined to form a comprehensive model. Analysis of inertial properties and fight data has led to the development of a multi-body dynamics model, where the ornithopter is modeled as a collection of chains of rigid body linkages emanating from a central fuselage. In the framework of this paper a flexible multi - body simulation and a novel experimental validation methodology is presented. To achieve high fidelity simulation and consider the flexibility of a flapping wing membrane, a Finite Element Approach (FEM) with a robust integration of the equations of motions (EOM) is used. The resulting ornithopter flight simulator is validated with experimental in flight data revealing the time history of the wing kinematics.