AF Fine Tune is near the bottom of the list with the Wrench. You get to set adjustments for each camera and each lens you own, plus it recognizes a TC/Lens combination. Check out LensAlign or FoCal.
My 200-400 has always front focused. I dropped it recently and got a loaner from Nikon through the NPS program. The loaner lens back focused at least enough I felt I needed to adjust it.
Nikon ViewNX2 places the focus point on the picture (if activated in the software) when the camera thinks it locks in on the subject. There are lots of times I think it still misses even when it indicates it found the target. Lately, I have been photographing mountain goats with both the D4 and D800 bodies. In good light, the single point focus will grab onto the fur's texture and I get sharp shots. In low light, focusing on the same point on the goat is less defined and the camera often yields softer images on the goat. They are essentially white with two dots for eyes and two horns off the top of the head. The red box might appear in ViewNX2. Sometimes, there is no box and the images is very sharp.
Your heron is a similar example. While there is some detail in the feathers on the chest area where you focused, you had a lot more contrasty details in the face area. Knowing they don't move too fast, you should have had plenty of time to put the focus point right on his eye, face and beak. I would have used the AF-S with a single point on the stationary heron, too. AF-C single point can still be searching for sharp elements even as it fires. In the field, I often snap a couple of quick shots of an animal as soon as I get the tripod set up just in case they move from the spot or turn their head. The first shots might only have the focus point somewhere on the body. After that, I take the time to adjust the focus points to the face and eyes.
The low light flight shots at an extreme distance with a 1.7 TC might be a challenge for you no matter how well you get your camera and lenses tuned up.
Personally, I'd rather enlarge a sharp shot in post processing than deal with a closer, soft image that was a result of using a TC. Everyone reading this forum will have their own opinion on this issue.
Lastly, some images are going to be soft as a result of "pilot error", or slight movement of the camera when you press the shutter button. This can multiplied by the extreme distance and TC.
Edit>>I assume you were in NM in December or sometime early in January. Since then, Nikon released a firmware update for the D4 that is supposed to help with AF tracking.