The analysis of the potential to improve performance of a methanol synthesis reactor through forced periodical operations by Nonlinear Frequency Response method is presented. The methanol synthesis in an isothermal and isobaric lab-scale CSTR is considered. First, the analysis was performed for single input modulations (in Part I), which showed that significant improvements can't be achieved. Here, the study is extended to analysis of simultaneous modulations of two inputs. All possible input combinations (6 cases) are analysed and the optimal forcing parameters, maximizing the time-average methanol production, were determined. For all combinations the improvement is possible, but for some cases it is not significant. The highest improvement is predicted for simultaneous modulation of the inlet partial pressure of CO and the inlet volumetric flow rate. This case, for which it is possible to achieve up to 33.51 % of methanol production, is analysed it detail and optimized using multiobjective optimization.