We analyze a cooperative wireless communication system with finite block length and finite battery energy, under quasi-static Rayleigh fading. Source and relay nodes are powered by a wireless energy transfer (WET) process, while using the harvested energy to feed their circuits, send pilot signals to estimate channels at receivers, and for wireless information transmission (WIT). Other power consumption sources beyond data transmission power are considered. The error probability is investigated under perfect/imperfect channel state information (CSI), while reaching accurate closed-form approximations in ideal direct communication system setups. We consider ultra-reliable communication (URC) scenarios under discussion for the next fifth-generation (5G) of wireless systems. The numerical results show the existence of an optimum pilot transmit power for channel estimation, which increases with the harvested energy. We also show the importance of cooperation, even taking into account the multiplexing loss, in order to meet the error and latency constraints of the URC systems.