I saw your post earlier and until today I had forgotten about a trick I learned for getting a good exposure when your lens is pointed towards an object which is in front of a bright background (i.e. a a dark feathered bird flying in the sky).
Ok this may sound obvious, but you need to use a speedlight (e.g. Nikon SB-900 or Canon 580EX) and a fast telephoto lens (if the bird a certain distance away). But not just a simple speedlight, you need to equip it with a flash extender. A flash extender is basically 2 pieces of plastic or metal or cardboard (if homemade) that attaches to the sides of the lens and allows a small rectangular piece of fresnel lens to be placed in front of the speedlight. What it does is extend the range of your flash by a few meters and focusing the light so that it seems to be 2-3 stops brighter.
When using this, you also need to set the speedlight to manual, not TTL. The stronger the light output of the speedlight, the longer it should reach.
You can buy one from Better Beamer here http://www.naturescapes.net/store/bette ... extenders/
or a DIY guide here http://blog.bahneman.com/diy_flash_extender
Otherwise, it will be very difficult to try and get a good exposure. The difference in stops between the bright sky and the dark feathers of the birds will be too much. If you expose for the sky, the bird will be dark. If you expose for the bird, the sky will be way overblown. Setting the camera to Auto-ISO will not help.
As for the color fringing, getting a good exposure will help reduce them. Another thing, use a polarizer.