Naruto Bijuu Mode FTW or "Draw." Why?
Naruto has most of the Kyuubi's chakra under his control. Not even Minato could barely stop Kyuubi when he was running on a rampage during the Kyuubi's Attack Arc. He even had to sacrifice his life just to stop Kyuubi's rampage to save hundreds to millions of lives.
Minato's arsenal consist of Space/Time Technique (FTG), Rasengan, and possibley Fuuinjutsu (Death God). Naruto in Bijuu Mode has an advantage over Minato's arsenal do to his Bijuu Coat, to protect him from physical damage, and his added reflexes do to Kyuubi's chakra. The only advantage Minato has over Naruto is his Fuuinjutsu, Death God, which could remove the soul of the caster and opponent as a last resort which ends the battle in a draw. It would be unknown and a gamble for Minato to use it against Kyuubi, but he would have to use it on Naruto removing him as a medium.