From what I've seen of them I'd go for the 400 f5.6 prime over the 100-400 IS every time. If you have a look you'll see that the prime is much sharper, it's also a smaller lens and feels great to use (your camera won't feel too lens heavy). The 400 f5.6 is very fast focusing and (I've been told) will still focus fast with a (taped) 1.4x tc in place.
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