Efforts to scale-up quantum computation have reached a point where the principal limiting factor is not the number of qubits, but the entangling gate infidelity. However, a highly detailed system characterization required to understand the underlying errors is an arduous process and impractical with increasing chip size. Open-loop optimal control techniques allow for the improvement of gates but are limited by the models they are based on. To rectify the situation, we provide a new integrated open-source tool-set for Control, Calibration and Characterization (C3), capable of open-loop pulse optimization, model-free calibration, model fitting and refinement. We present a methodology to combine these tools to find a quantitatively accurate system model, high-fidelity gates and an approximate error budget, all based on a high-performance, feature-rich simulator. We illustrate our methods using fixed-frequency superconducting qubits for which we learn model parameters to an accuracy of <1% and derive a coherence limited cross-resonance (CR) gate that achieves 99.6% fidelity without need for calibration.