I am pretty sure Harold is Tsukasa's father. Like in the one episode when they met Harold in .hack//SIGN he said a whole bunch of things that led to the conclusion that Harold is Tsukasa's father and also in the last episode Tsukasa said, "Im not afraid of you nor my gather." and Morganna then said, "Uhhhh...." it sounded like to me that Morganna recognized that. One more thing that can prove this, is Maha. She was made by Harold like Morganna and Tsukasa does call Maha Mother so it is likely that Harold is Tsukasa's father.