No it wasn't a clone. It wouldn't have made any sense for it to be a clone I remember thinking that back then although I never posted in those days. If it was a clone then there wouldn't have been any reason for Naruto to hide or for Itachi to ask Naruto why he wasn't running or for Naruto to ask why Itachi wasn't capturing him. It didn't make any sense for Kishi to make Naruto go off on his own but now I see why. Not that that makes any more sense.