The transport of cosmic rays (CRs) in the heliosphere is determined by the properties of the solar wind plasma. The heliospheric plasma environment has been probed by spacecraft for decades and provides a unique opportunity for testing transport theories. Of particular interest for the three-dimensional (3D) heliospheric CR transport are structures such as corotating interaction regions (CIRs), which, due to the enhancement of the magnetic field strength and magnetic fluctuations within and due to the associated shocks as well as stream interfaces, do influence the CR diffusion and drift. In a three-fold series of papers, we investigate these effects by modeling innerheliospheric solar wind conditions with the numerical magnetohydrodynamic (MHD) framework CRONOS (Wiengarten et al., referred as Paper I), andthe results serve as input to a transport code employing a stochastic differential equation approach (this paper). While, in Paper I, we presented results from 3D simulations with CRONOS, the MHD output is now taken as an input to the CR transport modeling. We discuss the diffusion and drift behavior of Galactic cosmic rays using the example of different theories, andstudy the effects of CIRs on these transport processes. In particular, we point out the wide range of possible particle fluxes at a given point in space resulting from these different theories. The restriction of this variety by fitting the numerical results to spacecraft data will be the subject of the third paper of this series.