I did this test accidentally when i was testing the 1ds3 versus my P30+.
I set up a still life shot and shot the exact same field of view with, (I think), the 85 on the 1ds3 and the 80 on the Phase. (No bitching here about the lenses not matching).
What I saw was, at about f11 or so, the 1ds3 had a much LONGER area in focus. At that point, I was simply testing what I'd call resolution or sharpness.
The Smaller Format will in general always have greater depth of focus. Imagine if I'd done that same shot also with a Deardorff 8x10; imagine how short the depth would have been if the focus distance was about four feet or so.
So the Nikon will win, in your situation. So you can cross that off your list, and then move on to the question about the quality of the lenses.
This is why people here come up with that silly phrase "3D effect" with medium format. They're seeing less inherent depth of focus with the larger format, versus 35.
Imagine if there was a 6x7 digital chip, and imagine how sweet that would look, shot wide open. But that's not what you're testing here; I simply started dreaming again.
Another higher-hassle approach would be to shoot two frames of each setup -- a front focus area, and then a back focus area, and then strip them together, but trust me, it sounds easy, but it's not. Very time consuming, but sometimes, it's just necessary.