You have an effective reduction of light with the TC, which will impede your focusing performance.
This link will explain the partial reduction of focus points according to maximum aperture and teleconverter strength.
Your lens combination does work; just with a lower hit rate and worse 3D tracking. I've shot with the same lenses, but a D800E body. There's a reason the expensive glass is expensive.
If you find the performance unbearable, you might try the 1.4 TC. Only about 5% loss of sharpness and, of course, much better auto-focus due to greater light transmission. You might need to use a different lens to achieve similar reach, but if the choice is between blurry subjects close-up and sharp subjects far away...