Advice

Agree, if nests are the highest point, that is where chickens will roost at night. Chickens poop at night and your nests will be full of poop. Then your eggs will be poopy and nasty. Cover the nests and put higher roosts. Sorry, I realize that does not address the issue at hand.

They don’t go in the boxes at night at all only during the day when they feel like it
 
So your 4 month old cockerel is going out of his way to attack the almost 3 month old pullets. Could you please describe that in more detail? Is he trying to mate them? That would look like him grabbing them and trying to climb up on their back. Is he trying to hurt them, chasing and pecking, trying to draw blood? Or is it more like he is trying to run them away? Is it just one or all of them at random? Are you real sure all those young ones are pullets?

Those are rough ages, lots of different things could be going on. Some people don't have issues with integrating but some do.

It sounds like the troublemaker is the cockerel. If you want to keep him, I'd isolate him for a week or so and see how the older pullets handle integration. My definition of a successful integration is that no one gets hurt. I'm OK with them avoiding each other during the day and even sleeping apart at night as long as they are not sleeping in the nests and are somewhere I consider predator safe. If they do OK I'd eventually release him and see what he does. He may be OK, you may need to keep him isolated until those young pullets start to lay. Or you may decide you really don't need him.

Thoughts on the coop and run. For eight hens you really only need two nests. More won't hurt but they should not be needed. The roost does need to be higher than the nests or anything you don't want them sleeping on. Not sure where yours are sleeping at night now. That can change when you add the new ones in there at night.

For integration it can help if the roost is high enough that the young ones can perch on it out of reach or the adults pecking their feet from the ground. It's pretty normal for my young ones to be on the roosts in the coop when I let them out in the morning while the adults are on the coop floor. They are avoiding the adults.

Adding clutter can help. That's things the young ones can hide under, behind, or over so they break the line of sight of the older ones. That can be in the cop but especially in the run.

But your basic problem seems to be that cockerel. He's what you need to deal with.
 

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