I like your #2 design. Nice graphics, too! I have a couple of suggestions. Just the things I would change, if I were building it for myself.
Looks like your run is tall enough to stand up in. That's great. I built one of mine that has an area only 5' tall. I always bang my head when I'm in that section. I'll be bent over trying to catch a chicken and when I stand up I get nailed.
I'd put the nest boxes in the wall where your window is now, move the pop door into the access door and put an opening window in the wall where the nest boxes was.
Heres why:
With the pop door moved over, it will give you the length of that wall for your roost.
With an opening window on the back wall, you can extend the roof overhang to give some protection from rain and snow. It will also allow you to have some cross ventilation between the pop door and the window, without putting a draft on the chickens, weather they are on the roost, or, in the nest boxes. When the weather gets really bad, you can close the window some, to keep the chickens more comfortable. I'd probably roof the run too. I have found shade is really important down here where I live. The chickens can handle the cold much easier than the heat.
Good luck with your coop. Looks great.