your going to have to make sure you use the right antibiotic for the symptoms you are seeing. Your flock has already been exposed to what ever it is, but you made the right move by getting mama and chicks out of there. I'll help by seeing if i can find something that will help you decide whats best to use for trearment. and VetRX will help with congestion like vicks vapo rub does.  I have some in my med. chest for my chickens. You would rub it on their nares and under their wings.
heres a link with some interesting info.  sure hope all will be okay.. will be praying.      
https://www.backyardchickens.com/forum/viewtopic.php?id=420511
1 more I just found.   
Sadly, there are many types of sickness that can cause these sort of symptoms.  Thankfully, there are readily available types of antibiotics at the feed stores that you can use.  However, here are a few tips that I have learned the hard way.
If you don't notice a dramatic improvement in 24-36 hours, you have the WRONG antibiotic.  don't continue wasting your medication and time using the wrong stuff.  
Once you have a sniffle/upper respiratory, plan on everyone in your flock getting it, whether you quarantine or not.  It is generally airborne, and will travel!  be cautious, and get enough meds for everyone.
Mix the meds in small batches that you know they will drink dry in 24 hours, if they are a bit thirsty in the morning, they will get a strong dose of the meds when you present the fresh batch.  (a bit thirsty does not mean dying of thirst.)
Check with your local store for a product called sulfadimethoxine.  it is a durvet product, just like duramycin, but it treats infectious coryzia in chickens.  Any time I see sniffles with eye complications I use this single product, and it is gone in days.  any of the 'mycin' products do not have ANY effect on coryzia.  The product is hard to find, I cant even buy it in my state, even tho it is cheap, 12.30 per packet.  I have to order it online, from Neeps.com, so I keep a supply on hand at all times.  Do not mix too strong, more is not better, in fact, too strong and it will kill.  Mix it according to directions.  Spelling is important, make sure you get the right stuff, not the stuff for dogs!  lol.   
Take comfort in the fact that the new hen may not have been the one to bring the problem too the flock, in fact sometimes the opposite is true.  Your flock may have been carriers of the organism in a dormant state, as they had built up an immunity, and the new hen, caught it from your birds, and it changed just enough to make your roo a bit ill.  Microorganisms are amazingly adaptive, and a quarantine is a good idea, but it will not solve all the issues, it may just delay them!  A bird that gets sick from your flock will have the same timing as if it came to your place carrying an illness!  It is sometimes impossible to tell which came first, the bird or the sniffles! 
Send for the sulfadimethoxine now, so it is on the way.  Try the locally available 'mycin' type antibiotics, and if they work, great, if they don't, the other will.  Finding the correct antibiotic is sometimes trial and error.
Good Luck!
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