Maybe that's why the shot of the deer are un-sharp, I shot it at 400mm.
Meh.
People underestimate how difficult it is to effectively use a long lens. You're seeing some motion blur, even at the butt-end of mama deer which otherwise would be sharp. The 100-400 is optically better than it deserves to be, but it's hard to see that unless you use excellent technique. Corner sharpness is mediocre wide open on full-frame cameras, but center sharpness is actually very good, and even the corners are decent from f:8 and good from f:11. It has Canon's first generation IS, which can't be used on a tripod and only buys you about two stops when hand-holding. Even if you lock it down tightly on a tripod, there's still enough play in the collar to hamper sharpness, so it's very difficult to get a really sharp exposure at 1/8th to about 1/125th sec. shutter speeds at the long end of the zoom range.
Despite all that, even on an older Eos-1Ds I'd occasionally get frames that were remarkably sharp, which told me that the issue wasn't the optical limitations of the lens, but my poor technique. The 100-400 zoom really rewards using a fast enough shutter speed, which is a lot easier with newer D-SLR's that still produce great images at ISO 800. I also find that for landscapes shot at the long end, taking multiple frames is important because frequently one frame is much sharper than all the others.