EOS 5D vs EOS 30D

I have a Nikon D200 plus 80-400 VR lens but am thinking of switching to Canon so I can get a prime lens of at least 400mm with IS for photographing birds, often in flight. With a given Canon prime lens, such as the 400/f4 IS, which Canon body would produce the sharpest image (cropped so they are the same size)? I like the 1.6 factor D200 sensor but do not know if an appropriately cropped image from a larger sensor would give an equally sharp image.

Also, is there is noticeable difference in autofocus under less than ideal light?

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Don Wigle
Ottawa
Canada