Using it on the 5DMKIII isn't difficult, but it will take longer than the fully automatic session on something like a MKII AND it will take longer than their manual suggests(at least on zooms). Granted I was running with the "tight" tolerance set, but it took over 20 minutes to do my 70-200 v2 on my 5DMKIII vs. about 10 on my 5DMKII.
Did you find much difference with the 70-200II after running FoCal Pro?
Understand that every lens and every body is different. Sometimes tolerances cancel, and sometimes they oppose and the mismatch gets worse.
The only lens I owned (of 15) that required "0" AFMA on all my bodies was my very old and well worn 300mm f/4L.