Hi, interesting read, I have come from an Alpa with Phase 1 to a D800 system and find I use it almost like a technical camera. I tend to compose in the viewfinder, tripod mounted of course, then switch to live view, zoom in to confirm focus and take the shot. Obviously that works for the style of pictures I take and may not work for you but I find it really straight forward. Like you I have mainly manual focus lenses, I have no problem focusing the Zeiss 135 f2 manually, very rarely am I off when I check in live view.
It's a great system for what I want and sounds like it is for you too, have a play with live view as RVB suggests it's just another tool but I find that once I had tried it I liked it!
Mat