I did all of my 1D X calibrations with FoCal, the results were quite good (benchmarked against LensAlign for a couple of lenses, the 24-105L and 85L II, IIRC), and hold up with real world shooting. But...I did the image capture myself, since there was no 1D X support at that point, and then when there was (when I was calibrating my new 600 II), I tried the Mac beta version for the first time, it didn't work (bug since fixed), so I shot that manually too. I used FoCal's manual mode. To be honest, the fit calls by FoCal ranged from good down to poor, I suppose because I oversampled (83 shots per test), but visually, it was obvious from the curve what was the correct AFMA. I did have to eliminate a few obvious outliers (camera shake, presumably, from bumping the tripod).
Given that there's no full auto for the 1D X, it's easier just to shoot the test shots manually (takes me ~10 minutes for the 83 shots, so testing a zoom lens at 4 focal lengths and 2 distances takes less than 1.5 hrs). I have done some of the other tests tethered (multipoint focus, for example).