But what if he was completely destroyed by those Omoyoudon
If anything Sasuke is the one who'll give him his arms back as its the yin that creates form out of nothing. NAruto used what people already had and gave life to it.
So how do you explain kakashis eye? He made a new one from nothing.
Naruto will heal those wounds as well. Naruto can create matter from nothingness, seen with kakashis eye and was able to heal a certain death state gai. Minato will recover so long as naruto heals him.