Time to go?

My 28 assorted chicks turned 3 weeks today, and the 11 assorted that followed will be 2 weeks wednesday. I have put them in the run where my two older girls can see them a few times, and even put Alice in with them (13 week australorp vs 2.5 week barred rock was a sight to behold. Little chicken was feelin her oats!) I dont even try to keep them in the brooders anymore-they roost on the edges 99% of the time now. (This is a good time to mention how happy i am for concrete floors and clorox). They enjou outside time, but the younger ones can still get out through the wire if they try (and they do, despite the 40x20' run they have). Id rather not split them into groups since the pecking order has been sorted. There is no way to modify the run any further-we are $1000 in the hole on it already (most expensive eggs ever). The coop is nearly done (needs roosts and nesting boxes).

So how do i transition them? Lock them in the coop for a week? Keep them inside longer? Put them into the run in daylight and coop at night? I woke up to a orpington sleeping with my husky mix (meaning it escaped the brooder, jjumped a babygate, and went through the whole bedroom in the dark). I think they are outgrpwing the accomodations.