Yep, I will paint the interior. I have a bunch of exterior latex paint leftover from the studio, so the inside will be a lovely butter yellow colour.
I agree that east/west windows sound like a good idea. Unfortunately, the other half of the coop is in the way of west facing windows, and light from the east would be blocked from the roof extension I now have planned (curse you all!). South facing windows are nice to add some warmth - we are far enough north that all of our winter light is coming from the south (blinds me all morning in my south-facing office). In my house, the room with the best light is the one with the north facing window. Most of the wind in this area is blowing to the south east (meaning if you face north west, you're getting it in the face. Forgive my explanation, I am no meteorologist.), so west-facing windows kind of suck. South is the way to go. I am adding the north ones for good cross-ventilation.
Re: nestboxes. The rollaway ones are free, so I will give them a shot. I can always whip up some new and larger ones if these don't work well. I may well add some once the boys go to freezer camp and I remove the temporary wall.