Given a link in the three-sphere, Ozsv\'ath and Szab\'o showed that there is
a spectral sequence starting at the Khovanov homology of the link and
converging to the Heegaard Floer homology of its branched double cover. The aim
of this paper is to explicitly calculate this spectral sequence in terms of
bordered Floer homology. There are two primary ingredients in this computation:
an explicit calculation of bimodules associated to Dehn twists, and a general
pairing theorem for polygons. The previous part (arXiv:1011.0499) focuses on
computing the bimodules; this part focuses on the pairing theorem for polygons,
in order to prove that the spectral sequence constructed in the previous part
agrees with the one constructed by Ozsv\'ath and Szab\'o.Comment: 85 pages, 19 figures, v3: Version to appear in Journal of Topolog
