Event-Related Potentials are crucial for analyzing brain activity in EEG recordings. However, latency variability distorts averaged signals, necessitating advanced alignment strategies. Traditional cross-correlation methods use constant displacements but lack subsample accuracy and fail to capture non-linear temporal shifts. This study evaluates different pre-processing strategies for ERP single-trial matrices before alignment, including a novel iterative and robust ERP reference selection method and optimized filtering strategies such as non-linear, anisotropic diffusion. Variational 1D alignment, which allows non-flat displacements with subsample accuracy, is applied to synthetic and real EEG datasets, including P300 oddball experiments (visual and auditory). Variational alignment with optimized filtering and reference selection preserves signal morphology and enhances signal gain to match the ground truth in synthetic data. The structure of non-linear displacements contains peak-to-peak variability, allowing signal reconstruction without loss of critical temporal features. Applying this method to real EEG data reduces amplitude differences caused by jitter while maintaining key ERP components. This method significantly improves ERP alignment, potentially enhancing BCI applications, resolution, and pattern recognition, particularly in later-stage ERPs. Additionally, explicit 1D displacement estimation enables time-resolved jitter variance analysis. This approach may reduce auditory brainstem response measurement times and extend to EEG-like data, including OPM and MEG evoked potentials, aiding in ERP-based diagnostics.