My first reaction was to the foreground clutter in the test shot, which Joe mentioned already. While it appears that the grass is outside the center of the camera's focus zone it does pose a possibility for the auto focus system to become confused. Your target has plenty of contrast so any focus stutter would not likely be related to that.
If I were to try an evaluate this shot with the assumption that AF locked on to the face of the box, I would say that it appears to be back focusing. At that distance and f5.6 the DOF would be quite shallow so the point of focus could be between the box face and just in front of the tire. If that were the case then a negative MA would be in order. It's difficult to find a focus point in your shot, that's why I'm assuming it's where I mentioned.
In order to take away any variables that may make adjustments difficult I would first be sure the distance is correct and that there are no obstructions or wind, secondly be sure that your target is square to your camera's focal plane (sensor). The variables I mention are tricky which is why I picked up a LensAlign Mark II system for my 500L. The LA MKII made all the difference with my MK IV and 500L combo. I was able to get a very accurate MA when including my 1.4X TC as well.
FoCal is new and I've heard good things about it. It may be a very good choice for you, it just involves a laptop in the process.
I notice the mkIV can detect the addition of a TC when carrying out MA and it treats the combination as a seperate lens, the adjustment for which it stores in memory.


