It is possible the lens' focus is out of calibration. Focus mechanisms can wear with use or just get out of adjustment with a bump or even be mis-adjusted from new. This can be adjusted and corrected, worn or faulty parts can be replaced if needed.
IMO it's unlikely that the lens needs cleaning inside. Usually stuff inside a lens - even a lot - doesn't effect focus and sharpness very much... It causes flare, veiling, loss of contrast and reduced color saturation. If images showed uneven sharpness, that might indicate a decentered lens element or group, another problem that often can be corrected. But just judging from your sample images, there don't appear to be problems of those types. I doubt you'll find anything of significance, but you can inspect the inside of a lens with a flashlight. Just don't panic if you see some specks of dust here and there. Those are common and not a problem unless there's a lot... a whole lot!
You probably should just send the lens in and have it checked and calibrated.
However, there are other things you can look for first, to rule out as possibilites...
1. As already suggested, that lens' closest focusing distance is about 3.5 meters (11.5 feet). If closer than that, you won't be able to focus So, yes, be sure you simply aren't trying to focus too close. (Notes: For comparison, your 100-400mm's closest focusing distance is 1.8 meters/5.9 feet. Also, adding a macro extension tube will allow the lens to focus closer).
2. Do you have a filter on the lens? If so, try without it. Quality filters can be helpful in some situations, but cheaper ones can make a mess of images and some lenses simply don't work well with the filters (actually your 100-400mm is one that is pretty widely known to not work well with filters... even good ones).
3. You mention using a tripod and remote release, and those are good for tests like these. Are you also locking up the mirror? At certain longer shutter speeds (usually between roughly 1/30 and 1 second) mirror slap can sometimes cause enough vibration to give some camera shake blur in images. The 100-400's Image Stabilization should be able to correct for that. But the 400/5.6L doesn't have IS, so would be more prone to show any vibration effects. When using really long telephotos without IS, at times I've put a beanbag on top of the camera and lens to help prevent vibrations, too.
You didn't mention what camera you are using, but an APS-C 1.6X crop model is more susceptible to camera shake, than a full frame model would be. On the other hand, the larger mirrors in full frame models are more likely to give mirror slap effects (all have some dampening, I'm sure.... but it likely varies with different models) .
Also, Canon has published a white paper about the 18MP APS-C cameras being particularly susceptible to any form of vibration... They recommend using slightly higher shutter speeds to offset this, especially with the crop cameras with very dense sensors.
4. Hopefully you are using One Shot focus for those test shots. Be sure to restrict to only the center AF point. And If your camera has it, try using Live View. That employs a completely different method of focusing and is a good way to test the camera and lens.
5. Use a clean rag lightly dampened with a few drops of isopropyl (rubbing) alcohol to clean the electronic contacts on the back of the lens. Perhaps some oils or dirt on the contacts are interrupting communication between the camera and lens, effecting focus.
Those are things you can try yourself at no cost. Since the lens is less than a year old, it should still be under warranty, so I wouldn't hesitate to send it in to Canon for calibration, if none of the above helps.
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Alan Myers
San Jose, Calif., USA
"Walk softly and carry a big lens."
GEAR: 5DII, 7D(x2), 50D(x3), some other cameras, various lenses & accessories
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