well, exact model ot stepper motor is nonlinear and you have to take this into account. Wait me and I wil send you some articles related with modeling of stepper motors and their closed loop performance.
May be helpfull. If you need more information about PMSM modelling tell me.
I understand, if you are focused only over control of the phase currents you can model the system as simple R-L circuit as first approximation you can introduce the term of induced voltage and approximate the nonlinear term