>What focusing techniques are getting you best results...<
I never use the timer delay. Three seconds is probably fine for the short focal length lenses, but may not be with the 70-200mm. I don't like leaving things to chance, so I delay tripping the shutter for more than three seconds with all lenses.
I setup the tripod lower in height as long as it does not compromise the composition. If there is any breath of wind I also will shield the camera with my body.
I use Live View Contrast Detect autofocus initially, normally at the lens' widest aperture, but then proceed to verify that focus was acquired accurately by manually turning the focus ring marginally one way then the other. This provides me with a good feel for what peak focus looks like. Remembering that, I re-focus using Live View. Finally, I stop down to the aperture I intend to shoot at.
I am not so keen on viewing at maximum magnification. Therefore, I judge Live View focus at one step less than maximum. I use a loupe in order to cut out extraneous light, and magnify the LCD on the camera body.
There is a workaround for the soft Live View image when viewed at maximum magnification: set Sharpening in the Picture Control you are using to a high, or even maximum, value. The value will of course be tagged to the NEF, but you can always adjust it later in post.
What aperture are you commonly using? Any aperture smaller than approximately f/8 will visibly soften the image as a result of diffraction. Use of the tilt function of a tilt/shift lens will help to avoid this issue for scenes that lend themselves to the use of this type of lens.
Which head, in particular?
>My D700 and D3x shots seem better in focus<
The same image viewed at 100% is magnified to a greater extent with a D800 than a D3x, and to an even greater extent than a D700. Therefore, it is not surprising that the performance may appear reduced.