Anticipatory sympathetic arousal is often inferred from skin conductance responses (SCR) and used to quantify fear learning. We have previously provided a model-based approach for this inference, based on a quantitative Psychophysiological Model (PsPM) formulated in non-linear dynamic equations. Here we seek to optimise the inversion of this PsPM. Using two independent fear conditioning datasets, we benchmark predictive validity as the sensitivity to separate the likely presence or absence of the unconditioned stimulus. Predictive validity is optimised across both datasets by (a) using a canonical form of the SCR shape (b) filtering the signal with a bi-directional band-pass filter with cut off frequencies 0.0159 and 5 Hz, (c) simultaneously inverting two trials (d) explicitly modelling skin conductance level changes between trials (e) the choice of the inversion algorithm (f) z-scoring estimates of anticipatory sympathetic arousal from each participant across trials. The original model-based method has higher predictive validity than conventional peak-scoring or an alternative model-based method (Ledalab), and benefits from constraining the model, optimised data preconditioning, and post-processing of ensuing parameters.