This paper uses detailed computational fluid dynamics (CFD) modeling with the kiva-chemkin code to investigate the influence of injection timing, combustion phasing, and operating conditions on combustion instability. Using detailed CFD simulations, a large design of experiments (DOE) is performed with small perturbations in the intake and fueling conditions. A response surface model (RSM) is then fit to the DOE results to predict cycle-to-cycle combustion instability. Injection timing had significant tradeoffs between engine efficiency, emissions, and combustion instability. Near top dead center (TDC) injection timing can significantly reduce combustion instability, but the emissions and efficiency drop close to conventional diesel combustion levels. The fuel split between the two direct injection (DI) injections has very little effect on combustion instability. Increasing exhaust gas recirculation (EGR) rate, while making adjustments to maintain combustion phasing, can significantly reduce peak pressure rise rate (PPRR) variation until the engine is on the verge of misfiring. Combustion phasing has a very large impact on combustion instability. More advanced phasing is much more stable, but produces high PPRRs, higher NOx levels, and can be less efficient due to increased heat transfer losses. The results of this study identify operating parameters that can significantly improve the combustion stability of dual-fuel reactivity-controlled compression ignition (RCCI) engines.