Unfortunately, there aren’t any hard and fast rules governing where to focus to achieve “...corner to corner sharpness”. What you’re talking about is depth-of-field. The 1/3rd rule is just an approximation, though it sounds to me like you’re demanding more of yourself (and your photography) than just that. Besides, the 1/3rd rule doesn’t hold up at all distances. Whether something is perceived as sharp or not depends on several factors including the amount of enlargement and, of course, your own criteria for sharpness. Using the smallest possible aperture will certainly give you the maximum depth-of-field your lens is capable of producing, but it will also increase diffraction resulting in a photograph with great depth-of-field but lousy sharpness. There’s no free lunch (certainly not in photography!).
If ‘corner to corner sharpness’ is what you want, stitching might be your best bet. Depending on the scene, a tilt & shift lens (for Nikon, PC-E lens) can also help quite a bit. It is easiest to determine optimal sharpness at (or near) max. aperture because it is here where your depth-of-field is at its smallest. However, inaccuracies can result from lenses which have a considerable amount of focus shift. Concerning your LCD in bright light, a loupe is really an indispensable accessory. Those from Zacuto are generally considered the best (and also the most expensive). However, I’ve had good experience with the Hoodman loupes.
As far as your technique is concerned, everything sounds quite correct (with the possible exception of focusing at max. aperture). Live View with the D800E isn’t a pretty matter (I’m hoping the D810 improves on this). Using a loupe and focusing at 100% magnification helps considerably. By-the-way, if you change your ‘AF activation’ setting in ‘custom settings’ (A4) to ‘AF-ON only’, you don’t need to switch to manual focus each time you take a shot. Assuming your lens is set to M/A, the manual override will allow you to focus, and the ‘AF-ON only’ setting will prevent any re-focus when you release the shutter. I’ve gotten so used to using the AF-ON button to focus, I would hate to have to do without it.
All the best with your focusing efforts,