I think it many of you are right at the same time.
Nagato has to be still to concentrate and carry out the Rinnegan ability of that magnitude.
The balance of power in Naruto's world is that with the greater ability the greater the consequence. The drawback is that it depletes the body.
Nagato's body is neglected physically while his mind is in the other bodies. Which as we see is pretty much round the clock. So his main body hardly gets the sustenance it needs as in nourishment. Yes, this is where Konan comes in as she is the only one he trusts to watch over him in his immobile state.
The rod in Nagato's back is huge in that it allows him to transmit himself to the 6 Pain bodies from a greater distance and allow him to amplify it as well.
The 6 rods/wires are to help split his chakra to each body but give greater ability to manipulate how much power to individuals as needed. Yahiko's body being his preferred body since it's sentimental.
Here's the thing though.
When he first used his Rinnegan he may have blacked out because he went into that guy and caused the body's own neurotransmitters that the body and brain produces to go crazy or excited to the point that he caused an internal forced explosion. This would explain the pool of blood and blood from the eyes and mouth of the guy that attacked Yahiko that he killed.
But the reason why I say this is I looked up neurotransmitter.
This is interesting. Remember Jiriyah said his chakra was going crazy when he was stuck with a transmitter?
A chemical substance, such as acetylcholine or dopamine, that transmits nerve impulses across a synapse.
Adrenalin, adrenaline, epinephrin, epinephrine - a catecholamine secreted by the adrenal medulla in response to stress (trade name Adrenalin); stimulates autonomic nerve action
GABA, gamma aminobutyric acid - an amino acid that is found in the central nervous system; acts as an inhibitory neurotransmitter
neurochemical - any organic substance that occurs in neural activity
acetylcholine - a neurotransmitter that is a derivative of choline; released at the ends of nerve fibers in the somatic and parasympathetic nervous system
A chemical substance that is produced and secreted by a neuron and then diffuses across a synapse to cause excitation or inhibition of another neuron. Acetylcholine, norepinephrine, dopamine, and serotonin are examples of neurotransmitters.
We know that he is able to transfer himself much like Ino's ability. But it's beyond that in that in time he has discovered in using the rods he is able to use the best jutsus picked/has gained to not limit himself to just one body transfer like Ino's family. Thus expanding his Rinnegan use of ability.
Now I don't know for sure but this is a theory in why he stabbed Naruto with a rod. Is it his Rinnegan (genjutsu) that is keeping Naruto in a submissive neutralized state? Or is it that Pain has taken control over Naruto's body by way of the rod? The reason I ask this is if he is controlling Naruto's body by way of the rod is it because he is inhibiting the nerve impulses in Naruto via the transmitter rod in his hands?
Another thing to note is that Naruto's new RasenShuriken's attack is based on a cellular level in that the wind chakra severs the chakra and nerve channels in the body thus making the target unable to manipulate chakra at all.
Now if only Naruto can get to Nagato himself to use it. But hey that's what friends are for eh?
