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For pt.I see ibid., vol.39, no.1, p. 282-297 (2003). This paper illustrates a general method to formulate the equations for the analysis of commutations and of the effects caused by large step-wise perturbations, large change of parameters, and circuit failures in switching converters including transformers, feedback circuitry, and soft-switching cells. The matrix equations obtained by means of the modified nodal analysis-based method proposed in this work are useful for theoretical inspection of switching converters as well as for numerical simulations. The examples of applications concern the analysis and the synthesis of switching converters and show that the Compensation Theorem (CT)-based model may help in selecting circuit topologies valid for the circuit design.