This paper, second in the series, extends our analysis of networks of protein folding-unfolding pathways in vitro from the equilibrium, analytically the simplest, to "in-water" conditions, i.e., to the case when the native state of a protein is, as a rule, much more stable than the unfolded one. Protein folding rates and folding nuclei determined for such "physiological" conditions are of special biological and medical interest because of their relevance to misfolding diseases and other folding-related disorders. Given the native protein structures and their experimental in-water stabilities, the previously developed general theory (see paper 1 of this series) is applied here to compute the in-water folding and unfolding rates and outline the folding nuclei. Agreement between these calculations and experiment appears to be reasonably good.