I know this is Christina's thread but I feel compelled to comment on Dave Humphries focusing problems with the D7100. If the active focusing point is put on a subject that area should be in sharp focus and then becoming soft as the depth of field trails off. It is possible that your lens and camera do not match up well. Cameras and lenses have to meet quality control within a range. Most times all is well but if a particular lens happens to be a +3 and a camera is a +3 that puts the focusing at +6 and out of acceptable range. If the lens is a +3 and the camera is a -3 they balance out to perfect spot on focus. There are many other combinations possible providing varying degrees of focusing. You might think of sending the camera and lens to Nikon to be adjusted. What I described is why a professional photographer when receiving a copy of a lens that doesn't focus to his expectations will send it back for another copy until one is found to match the camera. I believe that your D7100 had AF Fine Tuning in the menu but my experience with that is that it can really mess things up.
I always use focus release without a problem. I do not use Active D Lighting that if for those who shoot JPEG to open the shadows extending the dynamic range. Shooting RAW I prefer to do that in post processing. I have VR set to on but rarely does it come into play because my shutter speeds are too high for it to work. I have the ISO Sensitivity set to Auto ISO with a minimum of 100, a maximum of 3200 and a minimum shutter speed of 1/500. I noticed in reading the thread that you wrote that you had yours set to a maximum of 1100 or 1000 and Christina in another thread mentioned the same thing. If you limit the ISO to 1100 in many instances the camera will lower the shutter speed, most likely too slow for flying birds. That may be why your flying birds were soft. In the bright light of Florida shooting BIF at a shutter speed of 1/2500 most time the ISO is over 1000.