We applied the parametric variance Kalman filter (PvKF) data assimilation designed in Part I of this two-part paper to GOSAT methane observations with the hemispheric version of CMAQ to obtain the methane field (i.e., optimized analysis) with its error variance. Although the Kalman filter computes error covariances, the optimality depends on how these covariances reflect the true error statistics. To achieve more accurate representation, we optimize the global variance parameters, including correlation length scales and observation errors, based on a cross-validation cost function. The model and the initial error are then estimated according to the normalized variance matching diagnostic, also to maintain a stable analysis error variance over time. The assimilation results in April 2010 are validated against independent surface and aircraft observations. The statistics of the comparison of the model and analysis show a meaningful improvement against all four types of available observations. Having the advantage of continuous assimilation, we showed that the analysis also aims at pursuing the temporal variation of independent measurements, as opposed to the model. Finally, the performance of the PvKF assimilation in capturing the spatial structure of bias and uncertainty reduction across the Northern Hemisphere is examined, indicating the capability of analysis in addressing those biases originated, whether from inaccurate emissions or modelling error.