Ma/Pa toad and Naruto knew he would end sage mode during the fight so they've clearly come up with tactics for it. Given that, I don't think he's using the nine-tails chakra yet. If he can't return to sage mode and exhausts chakra he'll use the Kyuubi. Except for anger, he's only accessed it due to need. I don't see it coming to that. Naruto isn't a sage in my book until he's mastered sage mode. To me that includes maintaining it, but I think he has.
We don't know how long it takes to recharge sage mode, or if he even needs to in order to fight Pein.
Already stated by others (with some commentary):
1.) If the real Naruto is there, and a clone is gathering nature chakra, Naruto will pop it and be back in sage mode. Since clones divide chakra evenly amongst Naruto's, then he'll get back a substantial amount immediately.
2.) I don't think the real Naruto is not there. I don't think shadow clones can make other shadow clones. Further, if he's not there, then I see no reason why he would run out of nature chakra.
3.) I don't know how still he can remain in Gamabunta's mouth. It's fiction, so we can assume it's possible. Now we have to assume it takes 10 minutes (whatever time length you want) to return to sage mode.
Can a shadow clone last that long against two Pein bodies including god realm? It's possible I suppose if Naruto has allies to fight for him such as the toads. This was specifically mentioned by Pa toad during training, that if he needed chakra during a battle without fusion, then he would need allies to protect him while he did gather it.