Hi, I agree with you that the image is not sharp. Having looked at it at 100% nothing is sharp. Is it the focus system? The lens? Or some other issue? Perhaps, in the spirit of helping, I can offer a view as a very satisfied 100-400 user. I also do not know your experience of telephoto lenses, so I'll look at four aspects before considering calibration. I come at using telephoto lenses from the point of view of having been a marksman in rifle shooting. To be a marksman (I was formally trained and spent years practicing), four attributes of high performance are necessary: settings; technique (holding, breathing and triggering); training; and practicing. I believe these four attributes are also necessary to perfect telephoto lens use.
Looking at settings, for a static subject I agree with you and set Focus S and Single drive, which are fine (I use them too). I too use a small focus box and mechanical shutter. For moving subjects, I set Drive to CL and Focus to C. I use AF-C Custom 6 with tracking sensitivity set to 0, speed tracking sensitivity set to 2 and zone area switching set to Front. This works for running dogs, galloping horses, racing cyclists (my daughter), kite surfing (my son) and other moving subjects.
Looking at technique, which covers holding, breathing and triggering. I hold the weight of the 100-400 in the left hand with the elbow wedged against the ribcage (this is for non tripod use). I have also removed the tripod mount to make hand holding more comfortable (and put black electrical tape over the screw holes). The camera is stabilized by my forehead looking through the view finder. I hold the body with the right hand with the elbow against the body. For breathing, I take a gulp of air, exhale it and at the bottom of the inhale, exhale cycle, when the body is relaxed and stable, take the shot (some marksmen advocate pulling the trigger at the top of the inhale rather than at the bottom of the exhale, but whatever one adopts both agree that pulling the trigger should be done either at the top or the bottom when the body core is stable, never between the two when the body core is moving). For triggering, one needs to roll the forefinger gently over the shutter release to avoid a sudden jabbing movement (the same as caressing a rifle trigger), which would cause a movement of the camera body (a movement that few OIS systems could compensate for. In rifle shooting it is a big cause of missing). I use a convex soft release to smooth the action (a convex vs concave release is down to personal preference).
Looking at training, where one pulls the settings and techniques together using any convenient subject as a target and then analyse the results. Initially, I took several shots concentrating solely on holding, then took shots concentrating solely on breathing, then shots concentrating solely on triggering, and then pulled all three techniques together over many shots. Once satisfied, one then needs to practice to keep the skills up and hone them.
Apologise if this sounds like I am preaching to an experienced user (and for the long response), but I often wonder why many people think they can buy a telephoto and obtain sharp results straight out of the box. That does not happen in rifle shooting and in my view neither in telephoto use. Once settings, techniques and training have been concluded and if the results are still unsharp then I would agree, look to the calibration of the lens.
Hope that helps. Here is a hand held shot within my first week of buying and using the Fuji 100-400 (hitherto the longest lens I had was the 55-200), albeit on a somewhat larger and easier target.
FL = 400mm (600mm equiv). ISO = 400. Meter mode = Multi. Shutter Speed = 1/280. Aperture = f5.6
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J.
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