David,
How did you go about creating a "calibration card" for focus adjustment? Did you work on your lenses at all apertures, or just wide-open?
Josh,
The issue may very well be that the 1Ds3 stresses a lens' resolving power greatly, and that the 24-70 is at it's max. However, I'm inclined to think, at least based on what I've seen both qualitatively from the 1Ds2 (there were comments when that camera came out that lenses couldn't keep up), and current problems with the 1Ds3, that it may be a focus issue. Interestingly, I have a 17-year old 300/2.8 that I still use a few times each shoot, at it still amazes me with the resolving power. The 1Ds3 doesn't even begin to tax the lens.