The only preventative I do is to feed them dirt from the run on their second or third day in the brooder and every few days after that. The gets them any probiotics the adults have to pass on to them, gets grit in their system, and gets them started on any flock immunities they might need. Basically strengthen their immune system from the start. In your case, by now some of those benefits would be gone, but not all. I don't think you did that. It's not that big of a deal, just a missed opportunity.
In your situation I would have swept the coop out, removed cobwebs, any loose stuff. Then sprayed it with a bleach/water solution soaking it pretty well, then letting it air out a few days before I put any animals in. Once the smell is gone it would be safe for them. Vinegar is a disinfectant but might need to be fairly strong to be as effective as a bleach solution. Still, it is not a bad choice.
My suggestion is to observe them and see if you have anything to treat. Now that they have been exposed to their environment they have been exposed. Even with you efforts at cleaning they would have probably been exposed anyway.
I'll mention an old thread. Someone in your position found a mass of insect eggs in the old coop. The mass response on here was kill, destroy, sanitize. Clean! They obviously were not mites, lice, anything harmful to chickens. While I agreed cleaning the coop was a good idea, I was saddened thinking about how much fun the chickens would have had chasing all that free protein when the eggs hatched.
