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I would try to do the micro focus adjustment using the approximate distance you think you will be using the lenses for. For example, if you have lenses ranging from 85mm to 135mm, typically used for portraits, I would recommend adjusting/calibrating those lenses at portrait distances, somewhere between 3 feet and 10 feet or so. Long lenses for wildlife may benefit more from adjustment at longer distances, of 30 feet or greater. Zoom lenses? I normally do it a the long end and short end and the results I got are pretty consistent. The way I do it, if push comes to shove, I would put the setting more a tad on the front focus side. Since in real life conditions, you don't use your lenses wide open all the time and by closing the aperture, you will get a little more depth-of-field from the focus plane anyway.
One thing, I learnt from messing with the micro focus adjustment for over a year. Slant targets, like a ruler at 45-degree angle may result in inconsistency of the AF feature. I would strongly suggest to use targets that are parallel to the camera. Books or DVD cases arranged in staggered position of varying distance from the camera would be fine. I don't have any relation with LensAlign whatsoever but that device works great and I could repeat the microfocus adjustment with consistency. It is not cheap however .
Hope this helps,
Edited on Dec 17, 2009 at 04:58 PM · View previous versions