That's awesome! I love your covered run!
And I ran into the same issue with warped, uneven wood when I built my coop from an old fence. I don't think there's a square angle anywhere! But, as uneven as everything is, I was able to get the roof level. Haha! No more building from scratch for this...
Here are my old nesting boxes made from file crates I had at work. I used a strip of leftover vinyl flooring to keep the nest material in the crate.
Now, I have your average, run-of-the-mill external nesting box. I wanted more room inside the coop.
ETA: Had to delete and repost because I...