I owned an S2 and used it with 24-120VR AF-S, it always focussed quickly and accurately.
I suggest checking Fuji for software updates as I remember early code versions of S3 did not operate correctly with Nikon VR. Perhaps the same upgrade will could be better with AF-S.
To test backfocus use a fast lens wide open taking a test shot of a ruler, length-ways using focus point at 15cm (say).
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