Head gasket

When I put the heads back on my 360 I used the head gaskets from a set I'd bought at a swap meet. I was in a hurry and they'd only fit if I flipped one over. Anyway the motor runs fine but I can't keep it from over heating at slow speeds. I've tried new radiator, shroud, electric fan, timing, all the usual suspects with no help. Can the head gasket be plugging an opening maybe? Seems like any other head gaskets I've used always had the top marked. Any thoughts? Thanks.