Scott,
I'm ashamed to admit that I've had the kit on the shelf for months and haven't started it. It's a nice kit, but some instructions would be nice.
After looking at my copy I think the 4 2 1/2 inch pieces are for framing under the main roof. The other two, I believe, are the angle braces for the roof support.
I hope someone else here will have built it and can give you a better answer.
HTH
Chuck