Cutting the top angle is going to be a pain - I know - if your miter saw does not cut 60 degree angles. What you will need to do is mark the angles with your square and then cut with a circular saw. Remember, it's 60 degrees off square.

Once you have your rafters cut, then you can simply attach the side support boards. NOTE: I left a 24 1/2" gap for 24" wide t1-11 - you may wish to leave a slightly wider gap for easier access to the upstairs coop - or you can cut your plywood down to fit.

Another trick here is to cover the bottom with chicken wire. These things are always easier done now rather than when you are inside the coop :)