The nonlinear R-MI/SO system identification procedure and the parameters of the MDOF system identified in Part 1 are examined in detail in this paper. A parametric study is conducted and the results are presented on the sensitivity of the system parameters for two key nonlinear responses—subharmonic and superharmonic resonances. The parameters are compared to determine the appropriateness of using a single set of system parameters for both response regions. A detailed comparison of the MDOF and the corresponding SDOF system results is performed. The knowledge gained from the SDOF and MDOF studies on the applicability of the R-MISO technique for the system identification of MDOF submerged moored structures is discussed. The results show that the MDOF extension of the R-MI/SO nonlinear system identification technique works well; the resulting system parameters are relatively constant and can be applied to the both the sub- and superharmonic regions.