Damage zones adjacent to or associated with faults are important to the geologic community because of their implications to hazards and their ability to preserve evidence for, and show history of, slip, fluid flow, and deformation associated with large strike-slip faults. We examine two fault zones in southern California where fault zone damage is expressed. We revisit the drilled crystalline core from the Cajon Pass California drill hole, 4 km northeast of the San Andreas fault (SAF), and 1 km north of the Cleghorn fault, to perform a systematic structural analysis of deformation and alteration associated with strike-slip faulting at the site. The core preserved 19 fault zones, 11 of which were not previously identified. The most significant fault is a fully intact steep-dipping fault zone at 3,402 m depth with potassium feldspar and epidote alteration. This fault correlates well with the nearby left-lateral Cleghorn fault. The extent of deformation varies within the core, and is controlled by the size of the fault zones intersected by the core. The extent of deformation varies and is controlled by the size of the faults the core intersected. We also examined the nature of right separation across the Clark fault damage zone along the Santa Rosa segment using a marker assemblage of biotite, hornblende-bearing tonalite - marble - bearing metasedimentary rocks - migmatite located in Coyote Mountain and the southeast Santa Rosa Mountains. Separation measured from this study is 16.8 km + 3.67 km / -6.03 km. Our measurement uses the updated location of the Clark fault in Clark Lake Valley and matches a distinctive lithologic contact across the fault instead of matching the diffuse western boundary of the Eastern Peninsular mylonite zone as previously used. We calculate the errors associated with projecting the contacts across Quaternary cover to the trace of the Clark fault, and consider a range of projections. Additional strain may have been accommodated in folds and small faults within the damage zone of the San Jacinto fault zone. Two large map-scale folds deform the marker assemblage near the San Jacinto fault zone and we tested whether Cretaceous ductile deformation or brittle late Quaternary right slip produced the folds.