My D800e's were fine before and they seem fine after. The AF in AF-C mode seems better to me. The lens fine tune stayed the same after the update. I did verify several lenses with the Dot-tune method and they tuned to the same value.
My cameras have always focused well in low light and still do. There was a rumor about added additional noise in high ISO shots, but I did a test from ISO 100 to ISO Hi 1 and everything looked real good when printed out to ISO 6400 and in the ISO Hi category, functional.