The pressing global need for de-fossilization of the transport sector, especially within the heavy-duty segment, has intensified the exploration of alternative clean fuels. In this context, methanol gained traction due to their renewable production pathways, carbon-neutrality, and are being highly promoted by the Indian government to reduce CO2 emissions. Dual direct injection compression ignition (DDICI) is an effective combustion strategy to use methanol in heavy-duty engines, which combines the advantage of high-efficiency compression ignition with the clean-burning potential of methanol. In contrast to spark-ignited premixed methanol engines, this strategy involves a diffusion combustion of the methanol flame, thereby eliminating knocking and enabling running with high compression ratios. This experimental and numerical study presents a comprehensive investigation into the DDICI strategy using methanol as primary fuel and diesel as a pilot for ignition assistance. The work benchmarks the methanol DDICI operation against baseline diesel operation, catering the required combustion chamber modifications, fuel injection strategy, system layout and capturing key metrics like thermal efficiency and emissions. The numerical study details the effect of swirl spray orientation, and positioning of the pilot injector, on the charge distribution and the ignition. The 3D-CFD models used for the simulation model are well validated against experimental results to capture in-cylinder combustion dynamics and emission trends. The experimental results demonstrate that methanol DDICI achieves a thermal efficiency improvement of up to 2.5-3.0 % at high load with NOx reduction of about 50 % at similar exhaust gas recirculation (EGR) ratio compared to the baseline diesel. Additionally, it demonstrated soot-free combustion and lower in-cylinder temperatures reducing thermal stresses. The introduction of swirl led to improved mixture formation, promoted gradual ignition and enhanced post-flame oxidation, thereby reducing CO emissions. Furthermore, the simulation results revealed that the reduced spatial separation between diesel and methanol spray plume facilitates faster ignition and smoother combustion. In this regard, the stagger angle of 12.5° with 9-hole nozzle resulted in lower maximum pressure rise rate compared to 22.5°, with similar levels of thermal efficiency and NOx emissions.