A comprehensive modeling and visualization study of flow and combustion is reported for a production four-valve-per-cylinder homogeneous-charge four-stroke-cycle spark-ignited engine. Coupled port and in-cylinder computations are presented for five combinations of valve deactivation, valve shrouding, and cam profile. Motored (induction and compression) results are compared with transient-water-analog flow-structure visualizations. A new flamelet model for homogeneous-charge turbulent premixed combustion has been implemented for fired engine simulations. Several issues in the application of CFD to flow and combustion modeling in practical port-and-cylinder systems are addressed. These include numerical inaccuracy, elucidation of the role of induction-generated flow structure and turbulence, and new insights into premixed flame propagation. The results demonstrate the capability to capture differences in flow structure, turbulence generation, and flame propagation resulting from intake variations for real engines.