Yeah.... I believe in making life difficult for myself. *bangs head on desk*
Adding the master on the second level behind the car port caused other problems: the area I'm covering becomes wider than it is deep, and so the roof planes the wrong direction. I'd need to drag the back wall back two squares in order to make it work, and that just makes it obscenely large.
By changing the order I put the roofs on, though, I managed to drop the number of black spots down to two small bits. I can live with two small bits.