The only other detail that I need to figure out is the skylight. Originally I had wanted to build a raised unit that straddled the ridge as shown in this post. I am realizing that I need something simpler though. My dad sent me a link to the website for New England Skylights (NES), a company in Watertown, Massachusetts that builds beautiful copper windows. They do many new and restoration projects all over New England. The two photos below are of a window made by NES that is actually very similar to what I had envisioned having on my house.
I love the low profile of this window and how it fits so seamlessly into the standing seam roof. I am going to do everything I can to reproduce this. Ideally, I would make it so that it is hinged at the top to allow it to open. Time will tell if i can do this though.