I bought my D800 from KEH as a factory refurbished about four weeks ago. I shot a wedding where the high ISO performance was exceptional, and the focus issue appears to be absent (haven't had time to do actual testing, but after about 4000 photos, it's looking ok).
I do feel for all those people who got the run-around and had to send their cameras back, some even multiple times. I sense this camera was in the pipeline before the tsunami, and was rushed into production just as they began to recover; so they probably weren't as careful as they needd to be with it. For what it's worth, I've been using Nikon equipment since 1969 and have not personally had a problem yet, and in recent years all my camera bodies have been factory refurbished models.