The VIP-2 collaboration runs an apparatus in the Gran Sasso underground laboratories of the Italian Institute for Nuclear Physics (INFN) designed to search for anomalous X-rays from electron-atom interactions due to violations of the fundamental antisymmetry of multi-electron wavefunctions. The experiment implements the scheme first proposed by Ramberg and Snow, where a current source injects electrons into a metal strip (the experiment’s target). In this paper we describe the structure of a Monte Carlo program to simulate a new upgrade of the experiment, where the anomalous X-ray emission is modulated by an arbitrary time-varying input current. A novel feature of the simulation algorithm is that the Monte Carlo program is based on a mixture of analytical and numerical methods. We report preliminary, exploratory results on the expected detection rate for different modulations of the injected current; these results are a starting point on the way to optimize the modulation scheme and indicate a large potential improvement of the detection sensitivity.