This is the second part of the study in the identification and manipulation of biochemical reaction limiting steps. The first part (Analysis and Optimization of Biochemical Process Reaction Pathways. 1. Pathway Sensitivities and Identification of Limiting Steps) establishes a link between biochemical reactions and the macroscopic fermentation process by using a set of amplification/attenuation factors which influence individually each reaction step. A sensitivity analysis uses these factors to establish the influence of each step on the process objective function for any processing mode. In this paper the optimal selection of the amplification/attenuation factors is examined, in formulations resulting in nonlinear programming.