what settings are you using with the AF system? The new system is so complex that you may be using multiple point without knowing it. Just to test the sensor try shotting with single point AF in the middle and see if it feel still soft?
Just a suggestion...
1DX, 24mm f1.4L II, 50mm f1.2L, 85mm f1.2L II, 135mm f2L, 24-70mm f2.8L II, 70-200mm f2.8L IS II : D800, D4, 24 1.4G, 35 1.4G, 50 1.4G, 85 1.4G, 24-70 2.8, 70-200 2.8 VR II