We present a methodology to identify single bunch dynamics in the presence of electron cloud (e-cloud) and head-tail interaction in the CERN SPS ring. The main purpose is to extract the bunch dynamics from measurements and to estimate a reduced mathematical model of vertical dynamics. This reduced model is useful in the design of wide-band feedback systems to control/stabilize the bunch in the presence of e-cloud and transverse mode coupling instabilities (TMCI). The system estimation method is applied to data from numerical simulations as well as machine measurements from the SPS MD data. We illustrate this with examples from initial applications of the identification technique and present the beam excitation and response measurement hardware set-up, with future directions and next MD plans.