Where do you want the lens to take you in bird photography?
this is a serious question and you've chosen 2 very expensive and optically brilliant lens.
I have used in the past both the 400 f2.8 and the 500 f4, i own and use the 600mm f4 presently.
Optically you can trawl the internet and compare and contrast image quality of all the canon super tele's and at the end of the day realise that optically they are all great.
You ideally need to asses what type of photography you want to focus on and work from there.
-for example if you are primarily using the lens for bird photography and not other routes- ie sports photography etc
-if you are buying a lens solely for wildlife/ birding then what are your targets?? _ are you going to be spending most of the time shooting from a hide on a tripod or are you wanting to go for a sunday walk with it over your shoulder and using hand held?
The 400mm 2.8 is optically great but you need to use a tripod or monopod with it, if your taking shots of birds on perches it can be used at 2.8 for tack sharp results. If shooting panning shots of birds in flight you can still catch moments at 2.8 but in reality its worth stopping down to try and catch a sharper image- light allowing that it. You will end up with the 1.4 x extender glued to it though and will always want to be closer.
The 500mm f4 is great and why it is probably the most popular birding lens, at f4 its fairly fast and fairly sharp, but you start to get tack sharp issues with the depth of field- f4 at 500mm gives you a very slim depth of field and if photographing a close subject (within 5-8m)- for instance small birds on a preset perch you will start to get only selective parts of the bird in crystal focus. You need to stop down to f7 or narrower. The 500mm is much better in my opinion for flight shots, giving you more reach and lighter to manover to track.
Its also worth noting the minimum focusing distance of the lenses- esp if using close perches and hides.
-the 400 2.8 will focus to 3m i beleive whereas the 500 has a minimal focus point of 4.5m. My 600mm f4 has a minimum focus distance of 5.5m! which on occasion has caused issues.
my advice would be to think about what exactly you want to photograph, if you want very sharp perch shots and use a hide id recommend the 600mm over the 400mm if you can get a deal on one, for an all round lens get the 500mm i really dont think you will miss the few f stop advantage you get with the 400 as the reach will be the main factor esp on a full frame body.
if you save by getting the 500mm you can always look for a second hand 300mm 2.8 which will be more usefull for tracking smaller birds in flight close up and hand held, or maybe upgrade your 5d to a 1 series body - the 1d mk4 has great tracking of moving subjects and 1.4 crop.
sorry ive been rambling a bit..
best idea is to rent the lens if you can find a reasonable priced place to do so , or borrow / trial from a friend?
I came into wildlife photography mainly through a photography based background/ interest so look far too much into the final image and sometimes lose focus on the actual scene/subject im photographing, everything has to be razor sharp for me to be happy with it so my advice is probably a little off for most wildlife photographers.
whatever lens you end up with, your sure to adapt your photography practice to it, as in how you end up photographing with it- ( i shoot sports and mainly surfing -hence the 600, but often walked with friends on sun afternoon bird shooting and the 600mm is not ideal for it, i can/ sometimes do use it handheld and have come up with techniques etc to stable it but it is heavy! now i spend a fair amount of time within field craft and hides)
hence the opening question where do you want IT to take YOUR photography.
mike
I`ll have to get one...soon !!
) but you need to be fit of either sex to wield this without a tripod for more than a few mins! Its not the immediate first choice for flight photography either. If the bird you want is close enough then the image from the 400 will out perform the 500 - but its not so often that birds are that close. You lose a little with the 1.4 but its not that noticeable unless you are comparing shots side by side. Where the 400 wins against the 500 is in poor light conditions - the 400 will still be taking shots when the 500 will be struggling and might need a bit more post adjustment. The 5D Mk11 has more pixels I think? So cropping to make up for the loss of 1.6 compression is not always noticeable either - unless you have shots side by side to compare. Its horses for courses ........ Hubby has the 400 I have the 500 .... I bite my lip when he is still taking shots in near darkness - he bites his when I am taking something further off than his 400 can reach 
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