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Right, focus shift is when the lens focuses at different distances wide open and stopped down. Since most cameras focus with the lens wide open, the actual photograph can be out of focus if you shoot stopped down.
Depending on which lens I use, I either shoot and check focus repeatedly until I get it, or for the very difficult lenses like this one, I will often use live view, even handheld, and compose on the rear screen, move the focus square to where I want the focus to be, zoom to 100% (I have this setting on the centre button in the multi-selector control) while holding the camera still, focus and shoot. If the composition is critical and the focus less so, I might switch out of 100% mode before releasing, to fine-tune the composition.
I never use the focus confirmation dots. I don't know how accurate they are, they might be fine, but I don't like focusing like that.