I have shot almost 3000 frames this week with my new D800 in slot canyons (low light) and in open landscapes here in Arizona. I have shot about 90% HDR with from 5 to 7 frames per HDR set. Almost all have been from a Gitzo tripod.
Every image is sharp as a tack.
You may have a focus issue or AF Fine Tuning issue with non-Nikon lens. I have shot almost all images with top quality Nikon glass. I did shoot some wide angle with my Tokina 11-16mm DX lens just to see how sharp the DX images are in DX crop mode. I have not yet compared them side-by-side with my D300 images with the same lens, but they look good at first glance.