I would just put them in the coop. Not on the roosts. They can sleep on the floor until they are comfortable enough to get room on the roost. I am too cautious about the size of your set up, but I think that is because your roosts are so low? Can you raise them up? Chickens rather like roosting higher.
If you lock them in the coop, do get down early in the morning to let them out. But seriously I don't think you will have any problems if they are getting along in the run.
Mrs K
If you lock them in the coop, do get down early in the morning to let them out. But seriously I don't think you will have any problems if they are getting along in the run.
Mrs K