A framework for supervisory cooperative estimation in multi-agent linear time-invariant (LTI) systems is presented in the companion work (Part I). We introduced a set of sub-observers such that each estimates some states with a given set of input, output, and state information. A discerete-event system (DES) supervisory control framework is used for cooperation among the sub-observers. The supervisor selects a set of sub-observers to successfully estimate all states of the multi-agent system. In addition, in presence of a fault in the system, the supervisor reconfigures the set of selected sub-observers to minimize the fault impact on the estimation performance. Our general framework can be applied to any multi-agent system including industrial processes. In the companion paper (Part I), our proposed framework for the supervisory estimation is developed based on the notion of sub-observers and DES supervisory control. In this paper (Part II), a DES-based combinatorial optimization method for selection of an optimal set of sub-observers is presented, the feasibility of the overall integrated sub-observers is validated, and the application of our proposed method in a practical industrial process is demonstrated through numerical simulations.