Step three: build the roof
Attach 2x2s between the walls for support as shown above.
With screws, just attach 18" long to 24" long 2x6s at a 90 degree angle; make several of these sections, and stack them to the width of the building. Add 1x4 support boards across the underside to hold the roof sections together. Now, another supporting 2x2 is added on the inside corner.
Next, mock fit the roof on the two walls to figure out a good place to mount it. I recommend a longer roof overhang on the window side. Then make a "roof lid" for the storage area: add two hinges on the side with the least overhang. If the roof edge looks too new, rip some old wood with a circular saw and attach it to the edges.
Step four: build back wall
Cut 2x6 boards to make the back of the coop wall. Screw them into the base and into the support 2x2. You will need a bevel to copy the angles from the roof onto the boards; a bevel can be easily made with a screw and two pieces of scrap wood.