The first thing I do when I buy a new (or used) camera is to check the autofocus using all my lenses and FoCal. Every camera acts a little differently, and some lenses are known for a wide variation in AF accuracy. I have had well over 100 EF lenses, and only about 6 or 8 did not meet the Canon specification of being within 5 AFMA points. Only two were off by more than 8 points, my 100mmL which is off about 10 points, and my 35mm L which was off 17 and adjusted by Canon to be right-on.
As for Canon having the right parts, they only need a few hundred. They replace the mirror boxes because its easier, but they replace them with refurbished ones. They likely send out a batch every week to their refurb company in Mexico or Wisconsin or wherever. There is nothing that says new repair parts will be installed in a used camera.