1. Naruto has been shown to run out of chakra, and once he does he' helpless. If you think that he can create the amount of clones you're describing without losing chakra before nagato (who also has an amazing chakra reserve) then you are severely overrating naruto's strength...
2. Chameleon moves, nagato isnt dumb enough to let naruto find him in his summon, he will be well away from the area, letting his summons and CBT do the work
3. Not the gedo statue, the soul dragon...Which a) naruto has never seen, so if he touches it
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and b) isnt made up of chakra so it will phase through anything (including clones) and c) is
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when absorbing its souls, so naruto wont even have time to react...If nagato uses the gedo statue then naruto is dead...
4. Nagato on his
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could have made the CBT large enough to capture an 8 tails naruto...Healthy nagato can easily make a CBT twice as big...Given the ammount of chakra/lifeforce that he's diminished over his life and the battle...