We have no proof that naruot was using his Amazing speed. In that form naruto is the fastest character in the series, kakashi would not be able to react to his speed let alone use this jutsu. The jutsu has a fast activation time for linear objects and not for moving targets. For all we know both the hokage have the speed to keep away from the jutsu. One might get caught partially but no doubt they got this.
Kakashi has Sharingan, you underestimate it.
Itachi not only was able to follow Naruto with his eyes, but he was able to counter his taijutsu with his own.
Obito was able to effortlessly counter both BM Naruto's and Guy's taijutsu ONLY thanks to the Sharingan. And Kakashi stomped Obito in taijutsu.
There's no reason to believe Kakashi's sight can't keep up with BM Naruto. And Kakashi's sight is all that is needed to Kamui.
Keeping his Sharingan activated puts a strain on his body and chakra.
That was a problem at the beginning of Part I. Even at the beginning of Part II Kakashi could fight for a whole night without even getting tired.
On topic: Kakashi used two Kamui in a fraction of a second when warping Susanoo's two arrows. Nothing stops him from ending this fight in the very same fraction of a second.