Gasoline Direct Injection (GDI) is a key technology in the automotive industry for improving fuel economy and performance of gasoline internal combustion engines. GDI engine performance and emission characteristics are mainly determined by the complex interaction of in-cylinder flow, mixture formation and subsequent combustion processes. In a GDI engine, mixture formation depends on spray characteristics. Spray evolution and mixture formation is critical to GDI engine operation. In this work, a multi-component surrogate fuel blend was used to represent the chemical and physical properties of the gasoline employed in the experimental engine tests. Multi-component spray models were also validated in this study against experimental spray injection measurements in a chamber. The spray-chamber data include spray-penetration lengths, transient spray velocities and droplet Sauter mean diameter (SMD) at different axial and radial distances from the spray tip, obtained using a PDPA system. The simulations agreed well with these spray chamber measurements, within experimental uncertainties. 3D CFD simulations of an SI engine were then performed using automatic mesh generation with selective refinement at boundaries and in critical flow regions. The CFD setup was validated separately under motored and premixed-charge conditions, as described in the companion Part 1 paper. Detailed chemistry for combustion and flame propagation was employed, as implemented in ANSYS Forte CFD software. A validated detailed reaction mechanism from the Model Fuel Library was used for this purpose. As identified in the companion Part 1 paper, CFD predictions resulting from the turbulent gas-exchange process, heat transfer and combustion were in good agreement with experimental results, using motored and premixed-charge fired SI engine conditions. A validated spray setup was added to this full engine setup to simulate GDI engine operations in this work. CFD predictions of the SI engine under GDI mode were validated with experimental data for cylinder pressure and heat release rate, over varying operating conditions of equivalence ratio, injection duration and spark timing. CFD simulations used the same spray and combustion model parameters for all the different operating conditions.