ok 1 :naruto: has 100% of his chakra
he makes 1 shadow clone so there are 2 Narutos with half the chakra
:naruto: 50% :naruto: 50%
if he makes 3 clones then there are 4 narutos at 25% chakra :naruto: 25%, :naruto: 25%,:naruto: 25% :naruto: 25%
according to this page
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you MUST keep all three types of energy in perfect harmony to use senjutsu which means that EVERY clone MUST have ALL three types of energy, not just nature.
This is further proven from narutos training in
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because if the clones didn't need to worry about balance pa frog wouldn't have to worry about hitting them to stop them from turning into toads. you turn into a toad when you take in too much nature chakra and can't balance it out with spiritual and physical energies.
Naruto started the fight with Pein knowing he had 2 shadow clones at frog mountain. that means his chakra was split up 3 ways and each clone had 1/3 of the originals chakra.
he's not fighting with 3x his chakra he started fighting at 1/3 because he had 2 clones on the mountain. the chakra in the shadow clones stay in the shadow clones until he disperses them. THEN he goes back into sage mode. it would be more accurate to say that he's fighting in sage mode 3 x as long as he normally would but he's not 3x stronger.
NOW he only has 1 clone at frog mountain so he could be fighting at 50% because the balance must be met in order to use senjutsu. he has 50% of his chakra now so he must be able to hold more nature chakra as well to maintain balance.
my point is that i think naruto started the fight at 1/3 power because of the 2 clones at the mountain. now there's 1 clone so he's up to 50%. and when he uses the last clone he will be at 100% of his chakra level and should (according to the manga) be able to use more nature energy which is only limited by how much chakra naruto had to start with for balance purposes.