Molecular dynamics simulations and rotational isomeric state (RIS) theory are used to systematically examine the effect of the regioregularity of monomer linkages and the size of the pendant on the rotational barriers, flexibility and chain conformation of substituted polyparaphenylenes including hydrogen, methyl, tert-butyl, phenyl, methoyl and benzoyl pendants (R=H, CH3, C(CH3)(3), C6H5, COCH3, and COC6H5, respectively). The influence of the substituents on chain structure and properties can be broadly distinguished based on the degree of cooperativity for rotation about the paraphenylene linkage necessitated by the steric demands of the pendant. For some substituents (R=C6H5, COCH3, and COC6H5), backbone and pendant motion are intimately coupled leading to thorny rod polymers. In general, the conformation of these polymers depends on the relative ratio of regiospecific linkages and on the distortions of the backbone bond angles necessary to accommodate the pendants. For example, the persistence length of the chain decreases by almost an order-of-magnitude when the ortho-hydrogen of paraphenylene is replaced by a benzoyl pendant. Furthermore, chain flexibility is restricted to specific regioregular linkages and dynamic distortions of the backbone phenyl linkages. The relatively large intramolecular barriers to rotational motion will result in long relaxation times, frustrating chain packing and potentially leading to kinetically limited metastable states in the solid and melt.