Nikkor 400 mm z f2.8 tc issue focusing in low-light

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I am struggling to get my Z9 w/ 400 mm f2.8 tc to focus in low light conditions. I have been in Grand Teton NP and Yellowstone NP photographing bears. In GTNP I was shooting handheld while resting on the front hood of my truck w/1/500 shutter speed, both f2.8 and f4, iso 2200, bear probably 50 yards or closer, before sunrise. The face of the bear is soft. I had a similar problem yesterday in Yellowstone. This time though the bear was backlit, minimal face light, but the bear much farther away, 100 yards +. I was shooting w1/2000 f4 (tc engaged). I tried dx mode and increasing exposure compensation as well. Images were soft. It seem that unless there is light on their face, maybe because thei bear faces are so dark, the camera can't seem to get a sharp focus... or more likely that I am doing something wrong. Ideas?
 
It would help to see some of the problem images but I would definitely recommend not shooting across the hood of a vehicle as that frequently leads to heat shimmer and thermal problems unless the vehicle’s engine has been off for a long time and is dead cold.

Hard to say without seeing the images but atmospheric problems from either long distances or local air temperature differences (e.g. shooting out of warm car on a cold day, shooting across the warm hood or past a hot muffler, shooting across sun warmed asphalt or other situations with temperature differences that stir up the air) are common reasons for soft wildlife images.

Are any parts of the image such as foreground or background trees, grass, shrubs sharp? If it’s focus system errors then typically some parts of the image will be sharp if there are any closer or farther image elements in the frame. If everything is soft then I’d suspect atmospheric issues like heat shimmer or just shooting across excessive distances and through too much, dust, water vapor, etc. which happens a lot with wildlife.
 
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