In this work, we validate the behavior of 3D Photonic Crystals for Structural Health Monitoring applications. A Finite Difference Time Domain (FDTD) analysis has been performed and compared to experimental data. We demonstrate that the photonic properties of a crystal (comprised of sub-micrometric polystyrene colloidal spheres embedded in a PDMS matrix) change as a function of the axial strain applied to a rubber substrate. The change in the reflected wavelength, detected through our laboratory experiments and equivalent to a visible change in crystal color, is assumed to be caused by changes in the interplanar spacing of the polystyrene beads. This behavior is captured by our full wave 3D FDTD model. This contains different wavelengths in the visible spectrum and the wave amplitudes of the reflected and transmitted secondary beams are then computed. A change in the reflectance or transmittance is observed at every programmed step in which we vary the distance between the spheres. These investigations are an important tool to predict, study and validate our understanding of the behavior of this highly complex physical system. In this context, we have developed a versatile and robust parallelized code, able to numerically model the interaction of light with matter, by directly solving Maxwell's equations in their strong form. The ability to describe the physical behavior of such systems is an important and fundamental capability which will aid the design and validation of innovative photonic sensors.