I am not a big fan of separating birds. I think it causes more problems than it solves. Yes you needed to pull the rooster. He was just a bad rooster, and needed to be culled. But as to the injured birds. Chickens are not the smartest of animals, and when a bird is separated, she becomes a stranger to the flock, and when she is all healed up and you want to put her back, you have a rough integration issue all over again, with birds being upset, vicious toward the "new bird". A single bird is the worst integration one can do, even if they were part of the flock. This is going to upset your flock, both that attacking birds and the victim birds all over again.
I am a believer in Blue kote, slap that on the injury and stick them back in the flock. If they are really too weak to be in with the others, then put them in a cage inside the run during the day, Make sure there is shade, and in the coop at night. But pulling them completely away from the flock to the garage, is going to cause a lot of problems again with this flock.
I think that if you have enough space for the number of birds you have, and you remove the rooster, you should begin to enjoy your flock again. The flock should settle down, and be peaceful. IMO get those two birds back in that flock ASAP, or cull them too.
Good luck
Mrs K