Minato Namikaze the 4th
Uzumaki Kushina Mother of Minato Namikaze
Uzumaki Naruto's father (Unknown)
Tsunade said that Minato Namikaze is much more similar than his mother. It means; Uzumaki Kushina mother of the 4th hokage. Then Tsunade said that Naruto does look a lot like his father. It means the 4th hokage is not Naruto’s father.
Naruto's father topic:
Maybe Jiraya has a connection with Naruto's father, that's why he said he think Naruto as his own grandson.
Maybe Minato Namikaze didn't use he's mother's last name because of family problem.
Naruto's father entrusted hes son to the 4th. And that's why the fourth sealed the kyubi in Naruto. Coz the fourth can no longer protect Naruto, that’s why he sealed the kyubi in Naruto’s body for future needs of the kyubi’s power. That is also why Jiraya is also helping Naruto on how to control the kyubi. And the kyubi is also protecting Naruto’s body so the kyubi won’t die as well. And that’s why he threat Sasuke if something happen to Naruto.
About Pein, I can't say that Pein has a connection with the Uzumaki coz it hasn't been state in the manga about he's history.