X-ray and neutron optics both lack efficient ray focusing capabilities. An x-ray source can be made small and powerful enough to facilitate high-resolution imaging while providing adequate flux. This is not yet possible for neutrons. One remedy is to employ a computational imaging technique such as magnified coded source imaging. The greatest challenge associated with successful reconstruction of high-resolution images from such radiographs is to precisely model the flux distribution for complex non-uniform neutron sources. We have developed a framework based on Monte Carlo simulation and iterative reconstruction that facilitates high-resolution coded source neutron imaging. In this paper, we define a methodology to empirically measure and approximate the flux profile of a non-uniform neutron source, and we show how to incorporate the result within the forward model of an iterative reconstruction algorithm. We assess improvement in image quality by comparing reconstructions based respectively on the new empirical forward model and our previous analytic models.