I'll try to keep it short and am assuming both start the fight with info on each other with no edo.
Animal Path: Naruto's KM clones can handle any summons that Nagato throws out.
Human/Naraka: Naruto's taijutsu can prevent capture of his soul, and even if he did he would be able to use chakra arms to keep it from being ripped out immediately like he has shown to be able to do. If I were him, I'd keep a SM clone on standby close to the real Naruto while KM clones handle the summons of animal path.
Asura Path: Nothing it can dish out can pierce through a full BM Naruto. Even in the cloaked mode, he is too fast to be hit by Asura's projectiles.
Deva Path: Naruto was able to resist ST in a 6 tailed mode, so he should be able to resist ST or BT in BM. CT wouldn't be a problem because Naruto's TBB can easily destroy the core. Nagato/Pain have never been shown to acutally move while CT is in effect, which would have helped in stopping Naruto, Bee, and Itachi from destroying CT in their battle, so I assume his movement is limited while using it.
Preta Path: This is the most difficult due to Naruto's BM composed of chakra and not chakra flesh. I'm not sure if Preta can absorb a TBB, but I am going to assume that it can. For one, a SM clone can easily nullify Preta's abilities, rendering them useless. Naruto just needs to get close for a frog kumite attack to devestate Nagato. Also, a TBB fired close to Nagato but not directly at him can cause Nagato to get caught up in the blast wave without being able to absorbe the jutsu.
In all honesty, I think a surplus of KM clones (about 20) can overwhelm Nagato into defeat. He couldn't do that in his fight against edo Nagato because he had clones at the different battle fields. Nagato isn't that mobile, so he can't dodge the clones, and he doesn't have a stellar defense so he can't just tank their attacks. You might say that ST is a good enough defense but if Naruto goes BM, he can easily tear through it since a 6 tailed naruto resisted it.
