I just ran a comparison of these 2 lenses. Both were new copies. I am surprised to find out that the 100-400 performed significantly better on my t3i/600D. This isn't what I was expecting. Any explanations? Details here: http://lebirds.wordpress.com/
I did not. Maybe that would help, but I didn't want to mess with a lens that was not mine. Also, playing with the focus manually didn't seem to change much. However, you may be on to something, because that prime did not seem too sharp!
Take a look at this page from DPreview and scroll down to where they talk about microadjusting. I know it is a different model camera and lens, but it still shows how much micro adjusting might be needed with a Canon camera.
I do not have any canon products, but my impression was that the change in micro adjusting happens in the camera, not in the lens, so you should not be doing anything to the lens by doing it?
Very surprised by your test shots, I have shot a number of copies of each of those and have never seen a copy of the prime perform so badly... Don't suppose there was a filter on the prime was there? I also notice that in some of the tests the prime is giving a slower shutter speed than the zoom at the same aperture. Did something change between shooting the lenses?
No filters were used, and the lens hood was extended on the prime each shot. The timestamps on the Av mode shots were Prime at f/5.6 5:41:43, Zoom at f/5.6 5:37:38,
Prime at f/8.0 5:42:48, and Zoom at f/8.0 5:38:42. So the entire sequence was shot in less than 5 minutes, and I judged the lighting to be identical in each case. The tripod was not moved at all, and all were remote shuttered.
As far as microadjusting goes, it is possible that the prime was slightly front-focusing, but in reviewing all of my shots, it doesn't seem like it.