Heheh...going to part with the thing that got you those magnificent duck shots with the 1D? 
As others have noted it appears that you pretty much have your mind made up. Photography is about the moment. With a prime lens you may be left fiddling with composition and zooming with your feet and miss that 'perfect scene'.
The zoom range of the 100-400mm makes it a supremely capable lens, add to that the very silent (though I admit not blazing fast) USM and the two stop IS and you've got yourself a complete all-in-one lens for many purposes, appetizer, soup and desert included.
Previously I had this lens and nearly didn't want to let it go. Again, for the record the zoom range is fantastic. More so on a 1.6X crop camera than anything with a larger sensor or film. With the field of view of a 640mm lens at the longest end, you'll have enough reach for plenty of things. It's also light...not much heavier than the 300mm f/4 and thus manageable.
The push-pull zoom is a thing some may not like. I've found it fast and intuitive, and while I cannot confirm if it really does blow dust on the sensor, I'm afraid I have to say that it might. Dust spots appeared more readily on my sensor after I started using that lens. Of course YMMV. Also, some have mentioned that the lens seems to soften very near the 400mm end and the lens is really still very sharp at around 380mm or so.
My experience backs this up somewhat. I've found amazing sharpness at the 100mm end straight from wide open. It's very good in the middle range too but at the 400mm end seems to lose a bit of its lustre. That said the sharpness is more than good enough for most purposes. I view at 100% which may explain why I am dissatisfied with the sharpness. For printing I guess you'll never notice.
Another 'issue' I had with the zoom was that the bokeh often didn't look as nice as I'd wanted it to be, especially since the lens is fairly slow, going to f/5.6 at around 250mm+. The max aperture is simply not wide enough at those values to give you pleasing bokeh unless you're reasonably near to your subject.
The 100-400mm can't compete with my current 300mm f/4 IS from a sharpness point of view. And I also have a little niggle about the lens hood of the zoom. The 300mm f/4 is just so much more handsome with the built-in hood.
That said, those are minor detractions. If you want a zoom for wildlife (preferably not sports, unless in good light) then I'd say this looks like the perfect lens, for now anyway. I only ditched mine because I felt it didn't deserve enough use. Then I felt the itch to go super tele again and bought back a 300mm f/4 instead because I wanted to try it out. Life is all about the experiences.
fStopJojo has given a very glowing and convincing review of the 100-400mm lens but I would say that he probably has a stellar copy, something which I probably wasn't lucky enough to receive. In his tests the performance of the 100-400mm at the 400mm end exceeds that of the 300mm f/4 with a 1.4X TC. Yes, that's expected, but in my experience I found the results the other way around. Strange but true.
Also I note that the 300mm f/4 fares poorly with a filter mounted over the front...not sure if the 100-400mm demonstrates the same loss of quality with a filter.
Best of luck on your decision, whichever one you take. If you buy one second hand and don't like it you can sell it off for not too much loss. And when that happens you'll be left with some valuable experience anyhow...I'd say it's worth it. And when someone else asks such a question in the future, you'll be fully armed to help them as well! 
('engineering' a gift to show up at my doorstep, even if I have to pay for it, is a Good Thing(tm)).
