Resolution by % on D800

I find that my in-focus percentage isn't related to my zooming on the LCD.

Two things to keep in mind. 1) The image on the back is a JPG, so your JPG/Image settings do relate to how the image looks, even when you're shooting RAW. 2) When you're fulling zoomed in on the LCD, you're beyond 100%, so it's going to look interpolated and less sharp no matter how in focus the is.