Mixing controlled combustion of alcohol fuels has been identified as a promising technology based on their low propensity for particulate and NOx production, but the higher heats of vaporization and auto-ignition temperatures of these fuels make their direct use in diesel engine architectures a challenge. To realize the potential of alcohol-fueled combustion, a computational fluid dynamics (CFD) modeling framework is developed, validated, and exercised to identify designs that maximize engine thermal efficiency. To evaluate the use of thermal barrier coatings (TBCs), a simplified one-dimensional (1D) conjugate heat transfer (CHT) modeling framework is employed. The addition of the 1D CHT model only increases the computational expense by 15% relative to traditional approaches, yet offers more accurate heat transfer predictions over constant temperature boundary conditions. The validated model is then used to explore a range of injector orientations and piston bowl geometries. Using a design of experiments (DoE) approach, several designs were identified that improved fuel–air mixing, shortened the combustion duration, and increased thermal efficiency. The most promising design was fabricated and tested in a Caterpillar 1Y3700 single-cylinder oil test engine (SCOTE). Engine testing confirmed the findings from the CFD simulations and found that the co-optimized injector and piston bowl design yielded over 2-percentage point increase in thermal efficiency at the same equivalence ratio (0.96) and over 6-percentage point increase at the same engine load (10.1 bar indicated mean effective pressure (IMEP)), while satisfying design constraints for peak pressure and maximum pressure rise rate.