Mr. Clean wrote in post #9217710
No noob to MA, that's exactly how I do it, using the LensAlign product.
Okay, you aren't a noob to MA, but just because you adjusted it to super accurate focus using LensAlign doesn't mean that the real world situation will give a perfect subject on which to focus. It is very easy to end up with an image that is not focused on exactly what you intended due to the size of the autofocus sensor. I spent a couple of weeks working with my 50D when I first got it setting MA and then learning just how it focused in the real world. I went from disappointing images to sharp images. I had to learn the camera, I'm still in that process but of course photography is always a learning process.
I tend to work with focus a lot like I do with exposure when I think it is really critical, I "bracket" focus as well for lack of a better term. For example, I was shooting a very small mushroom with the 70-200 f/4 L at f/4. You can imagine that it is a curved surface and small and at f/4 there is little depth of field. I had to shoot multiple images trying to find just the right spot to focus on since the AF sensor could pick up a different spot than I wanted due to the small size of my subject in relation to the size of the sensor, and the fact the lighting was low. That is much different than shooting an image using LensAlign.
It is all about knowing the way your camera behaves under different circumstances and technique. When I perfect that I'll let you know. 
Cheers