Pistons should not be loose enough to knock when cold if things were done properly. What was the piston to wall clearance? If it was the pistons it would stop very quickly as it warmed. Do you have a priming shaft? I would try priming the engine when it's cold. Then firing it quickly after. If it knocks then it's more than likely the pistons. If it doesnt, it's more than likely a rod. What oil pump was used?
