I thought that was nagato at first too, but after this chapter it might be rikudou himself. Sir Derp Obito (and many others) theorized that the sage sealed a piece of his chakra in all the bijuu and I'm guessing that's what the rods reacted to. Nagato's rinnegan chakra disrupting Rikudou's perhaps?
That's the point where Naruto managed to sense that the real Nagato was else where as the rods gave him a direct line to him, boosted by his sage mode to get clearer reception. So those eyes are Nagato's.
It is Rikudou Sennin's silhouette/outline. You can compare it to the previous image we have seen of him. Although I am not sure why Kishimoto placed him behind Naruto. It was really interesting. Perhaps it is foreshadowing that Naruto will see/have a link to him or maybe even that Naruto might get the rinnegan. But I think that it showed the sennin because Naruto's chakra is quite similar to his with most of the Bjuu's chakra essence in him. I think that panel was the best in chapter 629...it's quite ambiguous.
Yeah I guess the Nagato theory slightly makes sense but Naruto isn't attached to any black rods. Plus it doesn't look like Madara is using genjustu on him. It is shown after a panel with most of the tailed beasts so I am assuming it is to do with Rikudou Sennin because his chakra essence is in all of the beasts.