I'd suggest rapid-firing at 6 fps and asking your subject to slowly come closer or recede. Some of the images will have the eye in sharp focus
On a more serious note, as Dylan said, if you're using it at or close to f/1.2 you shouldn't have problems.
1) A real solution (which could have many good uses) would be to be able to shoot with bracketed MicroAdjustment. A simple thing to programme.
2) As I wrote f/1.2 has no focus shift - at all. Shooting nearly wide however is not a way to avoid focus shift. Have not tested but expect by f/5.6 its zero (or virtually zero). Shooting nearly wide is begging to confron the focus shift (if shooting close portrait distance w/50L)
1) As Rahul also asked, can you elaborate? Sounds exciting, although I have no coding experience... I ask only out of curiosity at this point, I don't own any f/1.2 lens.
2) As far as I understand focus shift (courtesy of this forum and Neuroanatomist, and confirmed through further reading), focus shift occurs due to a mismatch in focus while metering (wide open) and while shooting (if stopped down). Therefore, when shooting wide open there should not be any focus shift, by definition. So there might be real world workarounds, but shooting wide open should definitely work.
2b) I have never used the 50/1.2L myself but the two technical reasons I mentioned caused me to suspect the focus shift claims haters love to harp on. It seems your personal experience confirms my suspicion.
edit: Roger at Lensrentals confirms the presence of focus shift. His methodologies are so spot on, and he has access to so many copies, I am inclined to believe him over and above everyone else.