Well that kind of sucks.
I am wondering if that may be the issue with my sister-in-laws cameras as well. Her focus issues are inconsistent as well so she has been double shooting just to make sure. The only good thing for her cameras is that they are both older models but she really can’t afford to replace one or both of them at the time.
I had problems with 2 cameras lately, both involving the AF systems. My 7D decided to try to commit suicide by jumping off the table and landing onto the concrete floor. Of course it landed in the most vulnerable spot, on the corner by the pop-up flash. Destroyed the AF drive mechanism and focus screen. Good thing it was under warranty :-). The other was my 1DX, it had a service bulletin involving a “potential” problem and my serial number fell within that “potential” group, so I sent it in to Canon.
I live about 75 miles south of a service center, so the turn-around was very quick. When I got it back, I thought something was wrong, so I looked into more. The focus worked fine and was no noticeable difference then before until you used a range selectable lens like the 70-200 2.8 IS. It would not focus to save its life. Tried all my other lenses and other camera bodies, only happened on the 1D. I was pissed.
Back to Canon it went, and 2 days later, it came back all fixed.
Wish I could tell you what they actually did, their repair form leaves much to the imagination of what they fixed, repaired or replaced.
So I think I am in the same boat as you, both my back up cameras are crops, so I don’t know what I would do if my main went down for a bit. I’m sure you can probably dig up a few smaller jobs to pick up a new 5D MK III or maybe a 60D for the meantime. I know its now 5DMKIII but at least it is full frame.