3 months old. Life is about to get exciting as those boys start puberty. The only good thing I see is that they are free ranging together now.
What are your goals? What do you want to happen? Do you want to keep all those boys?
To me the simplest thing is to get rid of all the boys except one. Let him and that one pullet continue to free range with the others during the day but sleep separately at night. You may run into a problem between that cockerel and your mature rooster at some point. But that pullet needs company so I'd try to keep one boy. I don't think it matters which one. Finish the second coop and train the pullet and him to sleep in it at night and see if you can continue free ranging during the day. It might work out, it might not. There are several things that could go wrong with this.
If you want to keep al the boys build a third coop and run, a bachelor pad, and keep the boys in there by themselves. No girls. That often works but no free ranging. This still leaves that one pullet. It's possible after free ranging with the others for a while, maybe a long while, she will merge with the main flock and be accepted, but there is no guarantee. So try keeping one boy with her in the second coop and see what happens.
You can try bringing in a few girls the same age as that pullet and integrate them with her and maybe one cockerel. Hopefully your second coop will have a big enough run so you can do that. I don't know how you feel about biosecurity and quarantine, that might be an issue for you bringing in older chickens. Very few places even try to sex bantams so if you get more chicks you run the risk of getting more males.
You can keep going the way you are and see what happens. Sometimes these things work out in ways different than expected. Since they free range the boys may not fight that much among themselves. They may leave the older hens alone so there is not that much conflict between them and that mature rooster. But I think you need to be ready to isolate one of more boys or that pullet on a moment's notice.