How do I focus calibrate a macro lens?

If you use the lens in autofocus mode at macro distances use those distances when calibrating, you can ignore the recommended minimum distance in the Target Distance Tool. If you use the lens more for say portrait images then stick with the recommended minimum target distances.

With macro type distances there's a smaller square target at the bottom of the target image file that can be used (download target image file) or you can use the very center section of the purchased "hard target" but will need to turn off target validation.

To turn off target validation, select Preferences > Tests (tab) > Target Validation (drop down) - No Target Validation and FoCal won't keep searching to recognise a specific the target design.

Macro lenses have high magnification at close range so any slight movement caused by the shutter can result in blurring, this type of blurring is interpreted as focus blur (FoCal can't tell it's caused by shot vibration). That being the case, ensure tripod is very sturdy, perhaps adding a weight to the tripod. The other thing that will help is adding light to the target as this will increase shutter speeds.