Stamina also is moreso the physical adpect of chakra and not the spiritual. Naruto has way more physical energy/stamina/chakra. May not be the same but its all connected.Wrong, stamina determines how much chakra the user can produce and control. More stamina = more chakra
Him having a ton of chakra gives him alot of physical energy. Him having much physical energy grants him much chakra and stamina. Its all in his genes and boosted by Kuruma in bijuu modes. May be due to his yang but thays just speculation.