This article addresses the control of a Multistage Stacked Boost Architecture (MSBA) feeding a five-level NPC inverter in a grid-tied application. A suitable control strategy was previously presented, in which estimated/reconstructed intermediary currents are used as feed-forward signals for the voltage controllers that balance the intermediate busses. While the reconstruction of the intermediary currents from the measured output current is easy to implement when the instantaneous switching signals of the NPC inverters are known, the real-time implementation on a digital controller must cope with the fact that these switching signals are generally not available at the base interrupt rate, but are usually generated in a peripheral unit, typically an FPGA-based modulator. The present paper describes an estimation/reconstruction method that overcomes this limitation and allows an appropriate estimation of the intermediary currents at the base sampling rate. The quality of the estimated signals is presented and analysed through comparisons of the measured and the estimated signals.