Hey Jeff,
Long time fan of your work here and I feel your current pain.
I've not read every thread in this post, but have picked up the last couple of weeks discussions, so apologies if I'm going over the same stuff but just a thought, have you tried live view focus? (auto or manual) does it show an improvement? Just wondering of it is something like the sensor moving (i.e. a problem with the cleaning system) or even the IS with the lens.
On more recent bodies if I have any doubts on the image quality/sharpness, I always double check that everything is satisfactory using live view, I've found nearly every time, live view contrast just beats the best phase detect can manage, I also check using x10 magnification and manual focus, mirror lockup, tripod, wired remote release to to show the setup is capable of producing sharp images.
I've also seen some pretty erratic phase detect results when the camera/lens combo is not properly MFA'd, once correctly dialled in the consistency and sharpness has returned. Having said that I've also seen one combo (50D and 300 f2.8LIS) that would just not work nicely together, it was my lens but not my body so that never got fixed.
One other thing that has caught me out wrt focus/sharpness and that's haze, caused by various circumstances, from hot sunny african days to shooting out of windows from a warm environment to a cooler environment, I've no doubt your experience would pick up on this but a couple of times I've had 100% "sharpness failure" on a series of shots and it's turned out to be haze - one such example is on a cold winters day (probably like summer to you!) shooting from a rear bedroom window of my house, at Redwings (European thrush) on a berry bush in my neighbours garden. Took me a while to work out that the cause of not one sharp shot was my neighbours hot tub, happily burbling away at ground level between my shooting point and the birds in the bush. 
Cheers
Kev