Autofocus tests are very hard to do because the competence of the photographer plays a pretty big role in it. So let me be up front. I don't photograph sports and its been a while since I've done birds in flight too. To help, I have overlayed the location of the active AF point so you can get an idea of what might have been a camera goof and what might have been operator error.
I set the ISO to be 800 to keep the shutter speed high. The first two are from the 70-200 f/2.8 IS II shot at 200mm wide open, shot handheld. These are 100% crops of a much larger frame. The AF point used as one of the off-center points (though still cross-type). I believe if you click on full screen, you will see the full resolution 1080p video.
Another series done with the 70-200.
I also had a chance to shoot with the new 400 f/2.8 IS II. The jump in focal length definitely starts to stress both the AF system of the camera and the strength of my arms due to the increase in weight and the fact I was handholding.
Again, you can reach your own conclusions.