What are dimensions of shed...in feet by feet?
How many birds do you have?
What is your climate? putting your location in your profile can really helps folks give better answers/suggestions.
I'd put the pop door going into the run towards the front of shed, 8" above ground level.
Poop board with roost above in back of shed, opposite shed people doors....nests underneath and maybe feeder hanging there too.
Where are you going to bring the power in?
You're going to need to put some ventilation in shed too....probably gable vents would work best.
Is there another window on other side of shed?