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I've had both. I have the 100-400 now. The 400L has excellent IQ - it also autofocus's noticeably faster the zoom. I switched, honestly, because I found a 100-400 for a great price. I thought that if I didn't like the zoom that I'd go back to the prime....so far I'm keeping the zoom for 2 reasons. The IS and the MFD. I keep this lens at 400 most of the time (I just lock it there). Once spring and summer hits, I'll use this while I'm out looking for birds to do some semi macro work (dragon flies/flowers etc.).
The 400L has better IQ, but you really have to be at 200% or better to even notice. It's really only even noticeable on a test chart. I haven't seen any real world differences. If you stop down the 100-400, it gets better too. I shoot at f/7.1 all the time. The 400L is basically as good as it gets wide open.