The Perceptual Eigenmode Distortion (PEMD), an extension to the Eigenmode Distortion (EMD), is a method for objectively evaluating simulator motion fidelity, developed at TU Delft. EMD investigates motion cue distortions, imposed by the Motion Cueing Algorithm (MCA), in terms of eigenvectors, which represent the dynamic modes of a linear system. In this paper, EMD is extended by a human perception model, which was assumed to help in assessing the various motion cue contributions. Additionally, a new automatic MCA tuning approach is introduced. The method is applied to a combined linear model of the Cessna Citation 500 for asymmetrical flight and the Classical Washout Algorithm (CWA). The automatic tuning algorithm is used to create an MCA parameter set and is compared to the current state-of-the-art method for objective evaluations, the Objective Motion Cueing Test (OMCT). A pilot-in-the-loop experiment was performed, with six pilots in the SIMONA Research Simulator, to assess three CWA motion configurations, which were compared in a double-blind pairwise format. Throughout each run, the Dutch roll eigenmode was externally excited with a gust of semi-random amplitude and direction. Two hypotheses were tested using subjective preferences and through measuring the Dutch roll suppression performance. Preferences varied between pilots and within-pairs, and similar results for PEMD and OMCT were found. A significant improvement in performance was found, however, between a no-motion condition and the PEMD. Therefore, PEMD seems to have considerable potential.