Hi Leigh,
both lenses are excellent. I've not used the 5.6/400 except for a few test shots. I've been using the 4/300L IS + 1.4x II for a long time. Very sharp, very light lens.
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I would go for the 4/300 + 1.4x. This will give you 2 focal length. Sometimes, when animals are closer, the 4/300 will be enough. If you use a crop camera like the 7/70D, it will be great. Depends on how shy the animals are where you live. Here in Germany birds require long lenses like 500/600 but in many places a 4/300 + 1.4x and a 7D will be a great setup. Also great for mammals.
The 4/300 is also a great lens for flowers and large insects as it has a magnification ration of 0.24x (I I remember correctly).
AF at f8 will only work with the EOS 5D Mark III and EOS 1DX (firware update may be necessary) and the older 1D models like the 1D Mark IV.
An alternative might be the 2.8/70-200L IS II with a 2x III extender. A bit more expensive but very sharp and popular. And you would have all the zoom range from 70-400.
Hope this helps,
Markus