This research examines the potential of a synthetic e-diesel and oxymethylene dimethyl ether blend in a heavy-duty single-cylinder engine. The main purpose is to find the optimal engine settings that maximize engine efficiency and minimize emissions. As the first step, a methodology was developed and applied to simplify the engine’s map into five characteristic points to be representative of the World Harmonized Transient Cycle, assigning weights to each load region. This simplification reported low error estimations for fuel consumption and NOx emissions over the cycle. After obtaining the five points, a drop-in analysis was assessed, where the fuel was evaluated with the same settings as diesel, revealing more advanced and shorter combustion with great reductions in soot emissions. Then, a group of three air management and three injection parameters was selected for optimization. A novel methodology combining Taguchi Design and Response Surface Methodology is developed and applied to find the best engine settings. By integrating these two methods, the research reduced the number of required experiments if only one method were used and maintained the goal of achieving higher thermal efficiencies with the new fuel blend compared to the diesel baseline. Significant statistical results were obtained in the Taguchi design, revealing the air management factors that most affected the responses; meanwhile, second-order models with high accuracy helped in finding the best injection parameters. Subsequently, the best settings were experimentally evaluated, and optimal conditions determined by the two methods were validated, confirming the effectiveness of the methodology. Optimization results revealed an improvement of around 2% higher efficiencies for the five tested points while achieving important average reductions of 28% less in NOx with additional decreases in CO, HC, and soot levels, all outperforming traditional diesel benchmarks. Finally, a well-to-wheel analysis using the simplified cycle confirmed a substantial reduction in carbon impact when replacing diesel with this alternative fuel. The successful application of this methodology to recalibrate an engine with an alternative fuel blend shows the potential of using these fuels in existing engines and offers a novel methodology that can be escalated and applied under the engine calibration context.