Hydrogen is deemed to be part of the future of road transport fuels. But the current SI engines, constituting about 56% of road transport engines, cannot utilize hydrogen without modification. HAJI technology has proven to be capable of providing reliable ignition and burning for hydrogen engines even in ultra-lean mixtures. A CFD model, equipped with a detailed chemical kinetics mechanism, is used to explore the viable regions for designing a new hydrogen engine. The initial and boundary conditions are provided by a lower dimensional GT-POWER model, simulating the engine. The 3D model simulates the HAJI flame propagation and knock. It is used to provide the designer with more accurate knock limits of the engine than GT-POWER predictions. The results show how a computational model of combustion can facilitate the design optimization of a hydrogen engine, with ultra-high compression ratio of greater than 14 and ultra-lean mixtures of lambda greater than 2.5, thus achieving high efficiency. The resulting engine has the power and flexibility of its gasoline counterpart.