Hi there and welcome to the forum!
I have tossed this in my mind for a very long time before this post, and it really depends on your priorities. Do you want a the best optical quailities and all the (usefull) bells and whistles of the new lenses. Or is weight, balance and convienece a top priority.
The 400mm DO is shorter and light, with having a longer focal length you can use the shorter 1.4 extender to achieve nearly the same focal length as the 300mm f/2.8 II and achieve better balance which aids in hand holding.
Bryan hasn't reported huge AF speed gains (actually quite hard to tell the difference) in the mark-II super-tele lenses so the 400mm will focus cosiderably faster than the at 400mm and 560mm. Remember, the 1.4 extender will cut your AF speed by 50% and the 2x extender by 100%. I'm pretty sure that there is not twice the AF speed between the 300mm and 400mm both native.
Also is 800mm f/8 important to you, you will either have to have a 1-series body, tape the pins or MF.
But IQ is not as good, more so in the contrast department than the sharpness. But it's still a downfall for this lens.
Do you need/want better IS? If you are like me and don't push you shutter speed much below 160th of a sec (birds are always statues) than this may not be as a big a deal for you, although you "probably" will get slighly better results with the new IS and the same shutter speeds.
Overall if I had to choose one or the other I would have a very hard time and would rent them both first. IQ is a big deal for me as much as AF speed is. Light weight is a plus also.
Cheers,
John.
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