
Can you blame them for being terrified of you?
If you want them to come around and trust you, you need to handle them gently and talk to them softly.
I currently have a bunch of juveniles out in my coop. Every single night I need to remove about 5 of them out of the nest boxes and another three or four off the edges of the poop boards and roost them manually. When I handle them, I slowly maneuver them into the correct position and gently lift them while talking softly to them. Over the course of many weeks they have relaxed much more with their response to this handling and aren't running away from me when I throw scratch to them anymore. This all takes time. But it takes slow and gentle movements.
You need to remember you are a predator and they are prey. Throwing them in a bag is not going to help your relationship with them at all.
I would let them out after they have been in there current enclosure for about 2 weeks. Then they will see that as a safe place to be and should return to it. When you first start to release them, do it about an hour or two before they would normally go to roost for the night.
It is a perfectly natural thing for a hen and a rooster to mate. If the cockerel is forceful with her and tries to just mount her without courting her or asking, she may very well tune him up. And he will deserve it! It takes time for a cockerel to learn what is expected of him with behavior and treatment of his hens.