Until recently, it was believed that the CP29 protein from higher plant photosystem II (PSII) contains 8 chlorophylls (Chl's) per complex (Ahn et al. Science 2008, 320, 794-797; Bassi et al. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 10056-10061) in contrast to the 13 Chl's revealed by the recent X-ray structure (Pan et al. Nat. Struct. Mol. Biol. 2011, 18, 309-315). This disagreement presents a constraint on the interpretation of the underlying electronic structure of this complex. To shed more light on the interpretation of various experimental optical spectra discussed in the accompanying paper (part I, DOI 10.1021/jp4004328 ), we report here calculated low-temperature (5 K) absorption, fluorescence, hole-burned (HB), and 300 K circular dichroism (CD) spectra for CP29 complexes with a different number of pigments. We focus on excitonic structure and the nature of the low-energy state using modeling based on the X-ray structure of CP29 and Redfield theory. We show that the lowest energy state is mostly contributed to by a612, a611, and a615 Chl's. We suggest that in the previously studied CP29 complexes from spinach (Pieper et al. Photochem. Photobiol.2000, 71, 574-589) two Chl's could have been lost during the preparation/purification procedure, but it is unlikely that the spinach CP29 protein contains only eight Chl's, as suggested by the sequence homology-based study (Bassi et al. Proc. Natl. Acad. Sci. U.S.A.1999, 96, 10056-10061). The likely Chl's missing in wild-type (WT) CP29 complexes studied previously (Pieper et al. Photochem. Photobiol. 2000, 71, 574-589) include a615 and b607. This is why the nonresonant HB spectra shown in that reference were ~1 nm blue-shifted with the low-energy state mostly localized on about one Chl a (i.e., a612) molecule. Pigment composition of CP29 is discussed in the context of light-harvesting and excitation energy transfer.