For system identification problems, such as noise and echo cancellation, FIR adaptive filters are mainly used for their simple adaptation and numerical stability. When the unknown system is a high-Q resonant system, having a very long impulse response, IIR adaptive filters are more efficient for reduction in the order of a transfer function. One way to realize the IIR adaptive filter is a separate form, in which the numerator and the denominator are separately realized and adjusted. In the actual applications, the order of the unknown system is not known. In this case, it is very important to estimate the total order and the order assignment on the numerator and the denominator. In this paper, effects of the order estimation error on the residual error are investigated. In this form, indirect error evaluation called "equation error" is used. Through theoretical and numerical investigation, the following results are obtained. First, under estimation of the order of the denominator causes large degradation. Second, over estimation can improve the performance. However, this improvement is saturated to some extent due to cancellation of the redundant poles and zeros. Third, the system identification error is proportional to the equation error as the adaptive filter approaching the optimum. Finally, there is possibility of recovering from the unstable state as the order assignment approaches to the optimum in an adaptive process using the equation error. Computer solutions are provided to aid in gaining insight of the order assignment and stability problem.