he used sage mode many times which is said to replenish his chakra. most of the chakra naruto is using is kyuubi not his own except when he counter madara's moktun and when he fight kyuubi.
No....
Kyuubi absorbs a portion of Naruto's chakra per clone.
MEANING.
That when Naruto split, the Kyuubi absorbed a ton of his chakra.
Sage Mode replenishes chakra WHILE he is in it, but the moment he exits it he's exhausted.
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Also, the clones he created each only have a portion of the real Naruto's chakra, yet they were fighting S-rank ninjas or skilled jonins like Toroi, ALL WHILE THE KYUUBI WAS ABSORBING HIS CHAKRA.
Yes, we are aware that Kurama stopped, but its due to Naruto's chakra levels that he can do such a thing. My theory is that Naruto has less chakra than the Third or Fourth Raikage WITHOUT the Kyuubi, since the Third was able to make the Hachibi exhausted. But Naruto has more chakra than Nagato.
Think about this though, Naruto's natural chakra level could be at the level of the Gobi, and let's say Nagato is at the Sanbi. That'd still be a huge chakra level.