In Part I of this paper, a multiple-input, single-output (MISO) model for the dynamics of practical premixed flames has been proposed. A corresponding method for identification of model coefficients was developed and validated against test data generated with a linear time-domain model, designed to be qualitatively representative of a practical premix burner. The method for system identification of a MISO model is now applied to time series data generated with Computational Fluid Dynamics (CFD) simulation in the presence of broadband forcing. The CFD model represents a generic, practical premixed swirl burner with multiple fuel injection stages. Fuel injectors are assumed to be acoustically “non-stiff”, such that pressure fluctuations will modulate the fuel mass flow rates. The flame dynamics is therefore influenced by fluctuations of the equivalence ratio as well as the mass flow rate of premixture at the burner exit. Results obtained demonstrate that system identification based on correlation analysis is well capable of differentiating between the various interaction mechanisms. Unit impulse and flame transfer functions corresponding to different signal-response relations can be determined in a quantitative manner from a single CFD run. A detailed analysis and physical interpretation of the response functions has been carried out. The results allow to draw non-trivial conclusions concerning a) the interactions of flame front kinematics and equivalence ratio fluctuations and b) flame transfer functions with an amplitude above unity.