Kakashi wins. Manga knowledge means he knows not to try to fight Tsukuyomi head on, whereas he has demonstrated enough skill with the Sharingan to counter Itachi's other genjutsus, as shown when he dueled Obito with genjutsu.
As for ninjutsu, Kakashi has shown himself being able to respond to Itachi's clone feints with clone feints of his own, as well as being able to tell when he's using explosive clones. Itachi himself would be in danger if he falls prey to a Raiton Bunshin. Katons can be countered with Hiding Like a Mole, or Kakashi using Suitons of his own, whereas shuriken can be blocked with Doton walls.
As for taijutsu, I don't see Itachi speedblitzing someone who was able to keep up with V2 jinchuriki (with shared vision and precognition), and Obito. Thus, all that's left is Susano'o and Amaterasu, the former of which Itachi can't maintain forever, and the latter of which Kakashi can defend against via blocking Itachi's eyesight with a Doton wall, a clone, dodge by burrowing underground, or even teleporting himself to the Kamui dimension. He could also warp it off of himself with Kamui like he did with Minato's Rasengan, assuming it doesn't hit somewhere beyond his vision.
In fact, Itachi is quite vulnerable to Kamui warps, seeing that nothing he has can adequately defend against the speed of War Arc Kakashi's Kamui. If trying to wait out and avoid Susano'o becomes too much trouble, I can see him just warping away the whole construct, Itachi and all, with a Gedo Mazo arm-sized Kamui.
