This paper proposes a 1D numerical/experimental study on a single-cylinder research ICE equipped with a hydrogen Port Fuel Injection (PFI) system. The experimental campaign covered tests at the fixed speed of 1500 rpm and different levels of load, from 5 bar to 11 bar IMEP, and of air excess, with a relative air-to-fuel ratio ranging from 1.4 to 4.0. A 0D/1D model of the investigated ICE is developed, including detailed combustion, turbulence, and NOx emission sub-models. In particular, combustion model is based on the fractal approach, k-K-T model is adopted for describing turbulent phenomena and NOx emissions are predicted by the Zeldovich mechanism. A sub-model was developed to assess the influence of Thermo-Diffusive (TD) instabilities on the freely propagating flame speed accounting for equivalence ratio, variable transport coefficients and reaction orders. This evaluation considered the impact of TD instabilities commonly observed in lean premixed hydrogen combustion on the flame front. The engine model calibration process enabled the comparison between numerical predictions and experimental observations, encompassing pressure cycles, burn rate traces, and main engine performance (air flow rate, IMEP, indicated efficiency, and timing of main combustion events). The model replicated the IMEP with an average error of 2.5%, gross indicated efficiency with an average error of 1.6%, main combustion angles with an average error of 3.8 CAD on CA50, and NOx emissions satisfactorily, showing high sensitivity to operational parameters. Nonetheless, less accurate predictions occur in cases with significantly elevated λ values (λ>3.6), which were attributed to the presence of thickened flames, where some assumptions inherent to the adopted combustion model may fail. Finally, a comparison between the proposed approach and the one proposed in Ballerini et al. (2022) is presented, and readers are provided with recommendations for further development of future models that account for Thermo-Diffusive instabilities in lean hydrogen combustion.