In this paper, the effectiveness for inferring the responses to electromagnetic threats of the finite difference time domain method combined with a multi-conductor, multi-shield, and multi-branched cable harness transmission line solver is validated by comparing simulation results with measurements performed on an equipped cockpit partially made by carbon fiber composite. A complete lightning indirect effects and high-intensity radiated field testing campaign was carried out in this cockpit within the scope of the European research and technology project Clean Sky 2 whose main goal is to reduce the aviation environmental impact by, for instance, building low-weight aircrafts with the increasing use of carbon fiber. Simulations are performed with EMA3D and MHARNESS obtaining very good agreement with measurements for a variety of observables and in a wide frequency range, thus proving the predictive capacity of these numerical methods for estimating the electromagnetic behavior of complex structures.