Ok I have some very detailed pictures and information regarding my issue but ill start with keeping it very short. I get very inconsistent results with all my lenses (50, 70-200, 300) and its becoming very annoying. I have tried several different focusing settings and shutter speeds. Even went as far as 1/1000th and above with IS off. From f3.2 to f11 gives decent results but also harder to tell if the focus is off. My main issue is shooting with the 70-200 at f2.8. It is extremely inconsistent to the point I can't even shoot at it. I had the same issues with my 300mm f4L to which I sold and now I am really starting to think my camera is off. I have had bad results with my 50mm too but I don't really want to compare those two because of the huge weight difference, That could easily be user error. My main concern is the soft focus at f2.8 with the 70-200.
Below are two images. The first one is default Micro Adjust meaning Disabled. The second Image is -11 or -16 Micro Adjust, Can't remember off the top of my head. Either way, The second image is much better and achieves this every time. Perfect right? Not necessarily. Now After shooting the iguanas several times, -16 worked great and then I walked away and started shooting other subjects like a car about 40 feet from me. Took the picture and it was soft. Took another picture of a different car, Soft. This alone tells me it's a distance issue. Leaving the micro adjustment off does give me the best results but today shooting the iguanas to which were perfectly lit in bright sunlight, The camera or lens just could not achieve proper focus. In the video I recorded, I tried everything from turning off IS, changing the shutter speed to even using difference focusing modes. Nothing worked but adjusting the focus to -16 for that moment and distance between me and the iguanas. I did a car show two days after getting the 70-200, Walk around shooting at mostly f3.2, f3.5, f4 and they were tack sharp, even the ones I took in Al Servo of all the cars leaving. But all my shots at f2.8 were soft. how does that make any sense? Any input would be nice and I can provide more images if you need. 
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