The propagation of waves in non-linear media (such as the lasers slabs in the final amplifier sections in Laser MegaJoule) is perturbed by the fact that the index of refraction of such media is modified by the intensity of the wave which, in turn, modifies the shape of the wave which, in turn, modifies the intensity of the wave... and so on. A localised small concavity in the wavefront due, typically, to non-perfect components, also perturbs the wavefront by creating a localised intensity peak further down the line. The computation of such modulation is relatively easy in vacuum, by simple wave summation according to Fresnel, but rather less so in non-linear media. This is because the above-mentioned index variations modify the actual optical path of the rays as compared to vacuum. For shallow defects, a simple but effective method is to proceed via the Fourier transform, of the defect shape. Individual spatial modes ("sinusoids") propagate with accurately-known amplitude variation. Modes are summed up after individual propagation, leading to accurate results. The amplification of such modes can be very great, leading to many-fold amplification of localised intensity peaks and, therefore, to potential damage to optical components. We explain the method, and compare numerical results with "real" simulations performed on MIRO (CEA's laser propagation code). Additionally, as we show, insight into the behaviour of defect amplification is gained. and accurate predictions can be made with little or no computational effort. This paper follows part I, given at Glasgow'96 : "Using First Principles in the specifying of optics for large high power lasers (I). Application to the MegaJoule Laser (LMJ)"(1).