A computer code, AGNI-3D, was developed for the modeling of turbulent, reacting flows with sprays occurring inside of a Wankel engine based on unsteady, three-dimensional computations. The primary objective of the present study is to assess the limitations and capabilities of AGNI-3D in predicting the combustion characteristics of the stratified-charge rotary engine (SCRE) that is being developed at the John Deere Rotary Engine Division. This engine has been modified recently with the inclusion of a second ignition source to supplement the standard pilot ignitor. Experimental tests of the modified dual-ignition Wankel engine demonstrated a 7.5% reduction in brake specific fuel consumption (BSFC) at low loads. Additional reductions in BSFC at high loads were limited by the onset of combustion instability. Since our interest in this engine lies at higher loads, we have limited making pressure comparisons to those few cases where experimental pressure traces have shown normal combustion behavior and cycle-to-cycle repeatability. The numerical results show excellent agreement with those pressure traces obtained from the Bottom Top Center (BTC) pressure transducer. Combustion in a dual-ignition engine appears to be dominated by the contribution from the trochoid ignition. The computations also provide instantaneous spatially-averaged and local heat fluxes on the rotor, side walls, and the rotor housing. The heat flux from the gas to the rotor housing near the vicinity of top dead center (TDC) is observed to be higher than the corresponding flux to the rotor since the sliding motion of the rotor near TDC generates higher velocity gradients near the rotor housing similar to Couette flow. Comparisons indicate a need for significant improvement in the Woschni model, a widely-used heat transfer correlation in the performance analysis of a Wankel engine. The results of a limited-systematic study conducted with the variation of the overall fuel/oxidizer equivalence ratios, fuel-composition, intake temperature, fuel-injection and spark timings are also summarized.