This two-part manuscript presents a comprehensive methodology for the irregularity assessment of urban stone pavements. The proper road surface assessment using key performance indicators is necessary to plan appropriate maintenance strategies. However, there are no monitoring methods or evaluation criteria for stone pavements whose surfaces are more uneven than traditional ones due to their structural characteristics. Therefore, it is useful to define criteria for assessing irregularities considering the comfort experienced by road users and classify their conditions. This second part presents the geometric and comfort analyses of 40 urban branch profiles to describe pavement unevenness. In particular, four methods have been investigated: the International Roughness Index (IRI) according to ASTM E1926, the surface profile classification according to ISO 8608, the comfort index (awz) according to ISO 2631, and the straightedge analysis for stone pavements (SASP) proposed by the authors that is able to evaluate the effect of localized irregularities, taking into account different urban vehicles. In conclusion, four classes have been defined to describe geometric and comfort conditions that can support road manager decisions in order to implement an effective pavement management system.