Looking at the example you supply I think I see part of the problem. I know the photo is small, and I'm looking at it on a computer as a second generation but you re shooting on a bright well lit day. The eagles have white heads and the heads look to be a bit overexposed. Long lenses need to be spot on to get the max sharpness possible. Also, I would bet you cropped this a fair amount. These things will greatly hurt sharpness. As sharpshooter noted, there is no substitute for getting dirty to sneak up on the birds, to get the shot you want.

Also, why were you shooting at ISO 800 on a bright day like the
Good Luck.

RobertM, I had not seen your photo before my post.
Treadwl, does a good analysis.
Wow, those birds are really far away. Are they cropped? For sure expose for the white. Use your blinkies.
What is your goal? RobertM, you have a scene with some birds in it. I strive to always get a catchlight in their eyes. I've never even seen eagle. So I don't know their envirenmont. But you either need to get much closer or much longer glass. Can you get there before they come out and use a blind? With birds feather detail is critical but you are way to far for that. I can't see the sharpness since I'm on my phone. But if the birds aren't moving, they should be sharp. At that distance you are probably at infinity so should be sharp. But they may be out of focus if your lens is focusing beyond infinity. If the birds are stationary, use your live view at 10x and see if your photos get sharper. Of course as a test you can shoot anything at a similar distance. Let us know what you get. And in that situation do lower your ISO.

Larry

OK, here are a few things to check or try:

1. For a stationary bird, use a single focus point and place it on the eye of the bird.

2. You are shooting in Av, aperture priority. The sweet spot on that lens is ~ f/8-11. this will also get you a higher shutter speed. In direct sun at ISO 800, you should be at 1/1600 to 1/2000. That will eliminate camera shake.

3. Use Image Stabilization set to #1.

4. If these things don't work, look to see if anything else in the frame is in focus. If so, test that camera/lens combination for front or back focusing. I have had that problem with that lens.

5. If nothing in the frame is pin sharp, and there is no blur from camera shake or subject movement, then suspect that the lens itself is faulty. Some people find their 100-400's are a little soft, most do not. I have seen some very sharp images taken with that lens so I know it is capable. It may require Canon to recalibrate the lens to bring it up to specs.

One last thing: You state you have taken pictures up to f/40 which is n ot available on the 100-400, nor is f/4.0 if that was a typo. Are you using a teleconverter? If so, that may be the cause of loss of IQ...especially if you are using a 2X converter.