I give you tons of credit for taking on the mess they left... If the roostesr grew up together they probably already worked out their biggest differences but they may spat once in a while depending on how overbearing the dominant one is.
If you can borrow a long handled fishing net from someone you know, or buy a cheap on at Wal-Mart or kmart... they are invaluable when it comes to catching flighty birds.
Brightly colored treats (cantaloupe or watermelon) may draw their attention, even from a distance and get them back into the run.
You can use hay or straw bales stacked around the outside base of the run to provide wind protection and one in the run can give bored birds something the dig at. Though be aware that the one inside the run may absorb moisture and get mucky around the base if you don't have good drainage.