Have you considered having your 100-400 calibrated? I looked at some of your zoo images on your Flickr site and they don't seem to be as sharp as they should be. You seem to shoot with higher ISO settings than necessary, but even then the images should be sharper. They seem to be a little better when you stop down so that makes me wonder if your lens needs calibration. My 100-400 seems to be sharper than yours, even when shot wide open.
Here's a wide open shot I took at the zoo with my 100-400.
7D - 1/125s f/5.6 at 310.0mm iso400
One more shot wide open - this one at 400mm.
30D - 1/250s f/5.6 at 400.0mm iso400
Canon 7D, 5D, 35L, 50 f/1.4, 85 f/1.8, 135L, 200L, 10-22, 17-55, 70-300, 100-400L, 500D, 580EX(2).
Sigma 150 macro, 1.4X, 2X, Quantaray 2X, Kenko closeup tubes, Yongnuo YN685(3), Yongnuo YN-622C-TX. Lots of studio stuff.
** Image Editing OK **