The new method of the Spectral Web to calculate the spectrum of waves and instabilities of plasma equilibria with sizeable flows, developed in the preceding Paper I [Goedbloed, Phys. Plasmas 25, 032109 (2018)], is applied to a collection of classical magnetohydrodynamic instabilities operating in cylindrical plasmas with shear flow or rotation. After a review of the basic concepts of the complementary energy giving the solution path and the conjugate path, which together constitute the Spectral Web, the cylindrical model is presented and the spectral equations are derived. The first example concerns the internal kink instabilities of a cylindrical force-free magnetic field of constant α subjected to a parabolic shear flow profile. The old stability diagram and the associated growth rate calculations for static equilibria are replaced by a new intricate stability diagram and associated complex growth rates for the stationary model. The power of the Spectral Web method is demonstrated by showing that the two associated paths in the complex ω-plane nearly automatically guide to the new class of global Alfvén instabilities of the force-free configuration that would have been very hard to predict by other methods. The second example concerns the Rayleigh–Taylor instability of a rotating theta-pinch. The old literature is revisited and shown to suffer from inconsistencies that are remedied. The most global n = 1 instability and a cluster sequence of more local but much more unstable n=2,3,…∞ modes are located on separate solution paths in the hydrodynamic (HD) version of the instability, whereas they merge in the MHD version. The Spectral Web offers visual demonstration of the central position the HD flow continuum and of the MHD Alfvén and slow magneto-sonic continua in the respective spectra by connecting the discrete modes in the complex plane by physically meaningful curves towards the continua. The third example concerns the magneto-rotational instability (MRI) thought to be operating in accretion disks about black holes. The sequence n=1,2,… of unstable MRIs is located on one continuous solution path, but also on infinitely many separate loops (“pancakes”) of the conjugate path with just one MRI on each of them. For narrow accretion disks, those sequences are connected with the slow magneto-sonic continuum, which is far away though from the marginal stability transition. In this case, the Spectral Web method is the first to effectively incorporate the MRIs into the general MHD spectral theory of equilibria with background flows. Together, the three examples provide compelling evidence of the computational power of the Spectral Web Method.