In this work computational and experimental approaches are combined to characterize in-cylinder flow structures and local flow field properties during operation of the Sandia 1.9L light-duty optical Diesel engine. A full computational model of the single-cylinder research engine was used that considers the complete intake and exhaust runners and plenums, as well as the adjustable throttling devices used in the experiments to obtain different swirl ratios. The in-cylinder flow predictions were validated against an extensive set of planar PIV measurements at different vertical locations in the combustion chamber for different swirl ratio configurations. Principal Component Analysis was used to characterize precession, tilting and eccentricity, and regional averages of the in-cylinder turbulence properties in the squish region and the piston bowl. Complete sweeps of the port throttle configurations were run to study their effects on the flow structure, together with their correlation with the swirl ratio. Significant deviations between the flows in the piston bowl and squish regions were observed. Piston bowl design, more than the swirl ratio, was identified to foster flow homogeneity between these two regions. Also, analysis of the port-induced flow showed that port geometry, more than different intake port mass flow ratios, can improve turbulence levels in-cylinder.