Premixed Charge Compression Ignition (PCCI), a Low Temperature Combustion (LTC) strategy for diesel engines is of increasing interest due to its potential to simultaneously reduce soot and NOx emissions. However, the influence of mixture preparation on combustion phasing and heat release rate in LTC is not fully understood. In the present study, the influence of injection timing on mixture preparation, combustion and emissions in PCCI mode is investigated by experimental and computational methods. A sequential coupling approach of 3D CFD with a Stochastic Reactor Model (SRM) is used to simulate the PCCI engine. The SRM accounts for detailed chemical kinetics, convective heat transfer and turbulent micro-mixing. In this integrated approach, the temperature-equivalence ratio statistics obtained using KIVA 3V are mapped onto the stochastic particle ensemble used in the SRM. The coupling method proved to be advantageous in terms of computational expense and emission prediction capability, as compared with direct coupling of CFD and chemical kinetics. The results show that the fuel rich pockets in the late injection timing are desirable for triggering auto-ignition and advancing the combustion phasing. Furthermore, the model is utilised to study the impact of combustion chamber design (open bowl, vertical side wall bowl and re-entry bowl) on PCCI combustion and emissions. The piston bowl geometry was observed to influence the in-cylinder mixing and the pollutant formation for the conditions studied.