Because I don't know how familiar you are with your camera or how you've set it up for the nest se Ii'll use this photo as my start.
http://www.flickr.com/photos/carolynmue/8517053559/in/set-72157632883096221/
If you look at it you'll notice that the pole is pretty crisp so your lens seems relatively sharp & the page shows that you're using a nice high shutter speed so camera shake is a non issue. Now if we look at this photo
http://www.flickr.com/photos/carolynmue/8517042777/in/set-72157632883096221/
nothing is that sharp. Is it a heavy crop? I suggest that using that photo as the ideal one to use to try setting your camera to Av mode & selecting f8 so you have some depth of field going for you, but check to see what shutter speed the camera picks (depends on the lighting that day) & adjust the ISO if needed to stay above 1/1000 & better yet if you can get 1/2000 all the better but you don't need more than that. Now for the important part, set the AF to the single center point & using the photo as the example birders try to get the AF point on the eye and when they hava a steady hold on the eye they take the shot. You could however pre focus on the eye & then reframe before the final half presss needed to take the shot. If your camera's AF system is accurate that method produces the best image of the bird, which in this case is an Osprey but the idea is for any bird where you can use the eye as the focal point (plus the same applies for most animals).
Now re birds in flight, you need to set the AF system to AI Servo, not 1 shot, but you can also leave it there for stationary shots (my cameras are almost always set to AI Servo). This allows the AF system to track & predict where a moving target is relative to you as it flies or runs etc. You also might want to try each metering mode when shooting against the sky because the bright sky is leaving the bird underexposed a bit. I run into the same problem shooting model aircraft & make many exposure compensation changes as the light keeps changing throughout the day. EC can be your friend but it may be a bit more difficult to change on a Rebel compared to the bodies with a big wheel on the back. Also switch to Tv mode for flying shots & stay above 1/1000 if you can.
Back to the lens choices. The 400 f5.6 L is lighter than the 100-400 L IS but the IQ from both is so close that the versatility of the zoom makes it the better choice for most people. On a tripod both will be easy to use but hand held you'll need to really work on technique, and although panning takes a bit of practice I find it easier to get a sharp shot while panning than when shooting a stationary object. Expect a learning curve but the IS can be VERY helpful, but you need to remember how to use the mode 1-2 switch. 1 for stationary, 2 for panning side to side BUT off for panning up & down or sideways combined with considerable up / down.
You could also consider one of the current Sigma zooms like the 50-500 OS or 150-500 OS but their AF system isn't as fast as the 100-400 L & they don't hold their resale value very well. The 50-500 OS would be my choice between them but I'd plan on using it on a tripod most of the time.
Hope that helps.
"A skill is developed through constant practice with a passion to improve, not bought."
