I've calibrated my 11 or 12 lenses on my 1Ds MKIII maybe 7 or 8 times. Each time I tried different methods suggested by various people. On every occasion when I re-calibrated I found there was some minor adjustments needed again. Since I documented results with each cycle, I know definitively what changed and by how much. Finally, I came up with my own flow for doing this with great precision.
What I now do is set the camera up on a firm tripod and choose a slightly slanting target so that I can see changes in DOF. Next I shoot tethered to C1 Pro. In C1, I make the first shot as the primary variant so that with subsequent shots, I can view @ 100% the change in sharpness and point of focus in the comparison viewer window. In other words, I get to see 2 images side-by-side. I shoot wide open with all lenses. When I see an image is sharper at the correct point I'm focusing, I make that new shot the primary variant so that subsequent shots will now be compared to this reference. I continue micro-adjusting focus until I find the best focus. I find this method to be the most reliable and accurate. Usually, you will notice also that when the best focus is reached, micro-contrast will also improve, on some lenses, significantly.
Please give my method a try and let me know if you find it helps your calibration. I love the ability to micro-adjust and I wish my 5D had this function. Guess I will need to buy a 5DII just to be able to do this. I will not but another DSLR that cannot be micro-adjusted.
Good luck.
