The one time we've seen Kakuzu in battle, he was targeting multiple opponents with his attacks instead of just one, and wasn't in full health (He had one of his hearts destroyed by Kakashi before the battle even begun). Despite all this, Kakuzu still proved quite a match for Kakashi.
Of course, Kakashi has definitely gotten more skilled since his battle with Kakuzu, and even then, he didn't use the Mangekyo Sharingan. So it could be argued that he wasn't fighting at 100% in that battle as well.
All in all, I think Kakuzu's 5 hearts, threads, and Iron skin technique would be too much for Kakashi to handle and would likely overwhelm him. Though that's not to say Kakuzu wouldn't sustain some heavy damage.
So basically, Kakuzu takes this with high difficulty, IMO.