Don't feel to bad, I'm sure you did a good job on what you did, just missed something in the original assessment that wasn't obvious to you. The clicking is most likely a rod bearing. The wrist pin bearing is new so that just leaves the big end. Its possible (likely) that a small piece of the wrist pin bearing cage was missed and left in the engine when repairs were made and has caused damage to the other bearing. Removing the propeller hub without planning a complete disassembly won't tell you much at all.