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I've not used one, but I've read that the 100-400mm is a good bit slower at 400mm and f/5.6 than either the 400/5.6L prime or the 400, 500 and 600mm primes. That could be part of the problem. Practice is also key. I'm way, way better focusing super-teles than I was three-years ago.
Take a static image of some printed material posted to a wall to check you AF calibration at 400mm.
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