Personally I think the Chakra stamina is not created by the red-chakra, or even the seal. It's the red charkra and//or seal that make him be less good in blue-chakra moves, as displayed in several early episodes and in several 40-60 episodes too.
The red chakra , influancing the blue chakra was the key<-- to the stamina, because Naruto kept practicing techniques. They may have failed, but his stamina must have increased dramatically that way.
Especially once u realise that he's done THREE years of practicing just a couple techniques.