In Part I of this paper we have discussed new methods for the numerical continuation of point-to-cycle connecting orbits in three-dimensional autonomous ODE's using projection boundary conditions. In this second part we extend the method to the numerical continuation of cycle-to-cycle connecting orbits. In our approach, the projection boundary conditions near the cycles are formulated using eigenfunctions of the associated adjoint variational equations, avoiding costly and numerically unstable computations of the monodromy matrices. The equations for the eigenfunctions are included in the defining boundary-value problem, allowing a straightforward implementation in AUTO, in which only the standard features of the software are employed. Homotopy methods to find the connecting orbits are discussed in general and illustrated with an example from population dynamics. Complete AUTO demos, which can be easily adapted to any autonomous three-dimensional ODE system, are freely available. © 2009 World Scientific Publishing Company.