No, because Perfect Jinchuurikis are said to be immune to genjutsu since the Bijuu can always snap the host out of any illusion. Kurama's consciousness remains (which is why he can sometimes speak through Naruto's body), but Naruto has total access to his chakra. If Naruto takes all of the Kyuubi's, uses it as his own and then goes into Bijuu Mode, how would a Mangekyou Sharingan be able to suppress this chakra in use with a mere genjutsu? Just because all of the chakra is essentially in one pile, it doesn't mean that the Bijuu itself disappears within the host (that's why Killer B and the Hachibi can still speak to eachother even when Bee is in 8 tails mode), if you get what i'm saying.