I'd say Naruto will win this barely.
Itachi has the capabilities, experience & intellect to take on and beat ALMOST anyone in the Narutoverse but as iSaid, ALMOST anyone, that excludes Naruto..
Here's how:
Itachi, the genius that he is, will somehow get Naruto to look into his eyes on purpose. Tsukuyomi sets in and iReckon that Naruto will not be able to get out of this genjutsu as it is INSTANTANEOUS! The Kyuubi will not be able to overcome the genjutsu fast enough before it is too late.
*Itachi 1. Naruto 0.
In terms of speed, KM Naruto should be more than enough to be surpass Itachi, giving him the ability to dodge Amaterasu effortlessly.
*Itachi 1. Naruto 1.
Final trump card now, Itachi invokes his Susanoo as a last ditch effort to subdue Naruto. Armed with the Yata Mirror & Totsuka Blade, you probably think this would be the end of Naruto...
KM Naruto's speed will enable him to avoid the attacks from the Susanoo with ease.
From here, it becomes an endurance battle in which we all know who is going to win...
Itachi will not be able to sustain the Susanoo for long and Naruto will be able to beat Itachi with Rasengan or something the results are obvious. K.O.
Final Score:
Itachi 1. Naruto 2.
Conclusion:
Itachi's only chance in beating Naruto before the match becomes too long is to capture Naruto in Tsukuyomi initially. If not, Naruto takes the cake hands down.
Itachi + Tsukuyomi from start = Win
Itachi + Naruto dodging Like A Boss = Lose.
The probability of Naruto dodging Tsukuyomi every time is kind of slim, Naruto is not battling against a retard you know, hence Itachi will come up with a plan to trap Naruto in a situation where he cannot escape the Tsukuyomi = GAME OVER!