This paper presents a non-linear, dynamic model of the flexure-based transmission in the Harvard Ambulatory Microrobot (HAMR). The model is derived from first principles and has led to a more comprehensive understanding of the components in this transmission. In particular, an empirical model of the dynamic properties of the compliant Kapton flexures is developed and verified against theoretical results from beam and vibration theory. Furthermore, the fabrication of the piezoelectric bending actuators that drive the transmission is improved to match theoretical performance predictions. The transmission model is validated against experimental data taken on HAMR for the quasi-static (1-10 Hz) operating mode, and is used to redesign the transmission for improved performance in this regime. The model based redesign results in a 266% increase in the work done by the foot when compared to a previous version of HAMR. This leads to a payload capacity of 2.9g, which is ∼ 2× the robot's mass and a 114% increase. Finally, the model is validated in the dynamic regime (40-150 Hz) and the merits of a second order linear approximation are discussed.