Harmonic drive systems (HDS) are high-precision robotic transmissions featuring compact size and high gear ratios. However, issues like kinematic transmission errors hamper their precision performance. This article focuses on data-driven modeling and analysis of an HDS to improve kinematic error compensation. The background introduces HDS mechanics, nonlinear attributes, and modeling approaches from literature. The HDS dynamics are derived using Lagrange equations. Experiments under aggressive conditions provide training data exhibiting deterministic patterns. Various linear and nonlinear models have been developed. The best-performing model, based on a nonlinear neural network, achieves over 98\% accuracy for one-step predictions on both the training and validation data sets. A phenomenological model separates the kinematic error into a periodic pure part and flexible part. Apart from implementation of estimated transmission error injection compensation, novel compensation mechanisms policies for the kinematic error are analyzed and proposed, including nonlinear model predictive control and frequency loop-shaping. The feedback loop is analyzed to select the controller for vibration mitigation. Main contributions include the nonlinear dynamics derivation, data-driven nonlinear modeling of flexible kinematic errors, repeatable experiment design, and proposed novel compensation mechanism and policies. Future work involves using physics-informed neural networks, sensitivity analysis, full life-cycle monitoring, and extracting physical laws directly from data.