I am probably going to be very unhelpful! I use almost exclusively manual lenses on a d800E. This is not new to me . I am old and AF is a new fangled thing that came lately. I agree focus by eye is not easy in modern DSLRs, but it is better than in the microscopes and electronmicroscopes I used in my formative years. We learned how to focus by doing it and ruthlessly examining the results. Time and time again. And it took time for the eye/brain/hand system to learn.
My only tip from using a d800E is to use a magnifying eyepiece (DK-17M). I use the same part of my glasses lenses always (head position), I focus the view finder dioptre control with great care with my eyes at infinity focus, I watch the object I want in focus with fixed attention and focus in and out, my brain works out what 'focus' looks like and tells my fingers where to stop in the continuous focussing in and out. That's it, take. Check in the LCD at max gain minus 2. Not right/learn/try again/check/learn etc. That is my procedure all the time.
Of course with 36 MP and large apertures, f3.5 - 6.1 is my normal range, focus is more critical than with say a D3S at f11, because you can see when it is off. I only use lenses that I have checked and know do not have focus shift. There is no fine tune in MF, so if your lens has focus shift you have to use LV as then you focus with the lens stopped down to yout chosen aperture.
The green spot is misleading on the lenses I use so I ignore it. Also it would take my attention off the visual achievement of 'focus'.
Finally do I ever get shots in focus? Yes! Even of birds in flight! How? By taking photographs every day and being hyper-critical of my results.
Enjoy the ride, just keep taking pictures! Roderick.