It's not the fuel pump. And the ECU is NOT under the battery, though the advice of checking cylinder 3 circuit from the ignition coil to the PCM, and the injector to the PCM, are the best bet. If you've checked and replaced all these other items, and you did the checks correctly, then it's either circuits or wiring. Another thing you might want to check is the balance shaft, based on what you're description of the engine behavior is... but don't go and check this until you're absolutely certain all other avenues have been checked, as it's unlikely that would cause your misfire, but not impossible, since first order vibrations in the engine can cause your sensors to mis-read.