This paper describes the design of a control structure for a large-scale process known as the HDA plant. A steady-state "top-down" analysis and optimization of the process (described in Part I of this series of papers) was used to select 16 sets of candidate "self-optimizing" primary (economic) variables. In this paper, we focus on the remaining "bottom-up" steps, which involve the following: selecting where in the plant the production rate should be set; design of the regulatory control layer; design of the configuration of the supervisory control layer; and nonlinear dynamic simulations to validate the proposed control structure. Emphasis is given to the systematic design of the regulatory control layer which constitutes the backbone for the optimal operation in the higher layers. To perform the analysis, steady-state and dynamic models are necessary and Aspen Plus and Aspen Dynamics are used extensively. The final control structure is robust and yields good dynamic performance.