In this paper we perform an analytical and numerical study of the performance of a wave cycloidal rotor in irregular waves, with passively morphing foils and variable rotational velocity control. The performance is measured in two ways: Mechanical power, and fatigue damage in a sample stress hot spot located at the fixed end of the hydrofoils. We consider different strategies seeking to both maximise power extraction and reduce fatigue damage. To maximise power, we consider both constant and variable rotational speed. To mitigate fatigue damage, we consider, for the first time, morphing foils in the context of a wave cycloidal rotor. By testing these control strategies in isolation and in combination, and with the aid of high performance computations, we find that variable rotational speed, in combination with morphing foils, offers the best compromise to enhance power production with a reduced structural penalty on the sample stress hot spot. Hence, in this work, we demonstrate that novel control strategies, such as those proposed in this work, can hold the key in reducing the levelised cost of energy and accelerate the commercialisation of the next generation of lift-based wave energy converters.