I had a similar experience when i came from nikon to canon.
I used a d800 and 200-400 vrII, and had really good hit rates with 9 point dynamic focus (or center 5)
When i got a used 1dmkiv and used 500mmf4 IS, i expected to do atleast equally good, since it was a ''pro'' body and a prime lens.
I had a lot of issues to get images in focus both static and ones on the move.
Now things are improving and i use center point only instead of using an expansion with it.
But I think i may have been romanticizing the nikon experience a little bit also ( I had missed focus with that one on some important moments also), and maybe expecting too much of the new camera+lens instead of my needed improvement because it was less forgiving
(DOF calculator showed major difference between d800+400f4 and 1dmkiv with 500 f4 / 700f5.6.)
1dx+300 2.8 @ 30 meters gives :Total 1.68 m
In front of subject 0.82 m (49%)
Behind subject 0.86 m (51%)
1dx 400 2.8 @ 30 meters gives:Total 0.94 m
In front of subject 0.46 m (49%)
Behind subject 0.48 m (51%)
Quite a big difference !
For me it was even bigger of a difference:
Total 0.65 m
In front of subject 0.32 m (49%)
Behind subject 0.33 m (51%)
Now , and previously
Total 1.33 m
In front of subject 0.65 m (49%)
Behind subject 0.68 m (51%)
It's about half what i was used to , so my error(and the camera error) is less forgiven.
I used : http://www.dofmaster.com/dofjs.html for the DOF numbers.
As for the moon shot, i think atmospheric conditions play a major role there !, bad seeing can even make a 400 f2.8 look bad compared to a 120-400 sigma lens