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