This sounds like a respiratory infection and with the nasty smell it could even be coryza. Chickens don't really get colds like humans do. They may get better and seem healthy, but may be carriers of the disease and when stressed may show the symptoms again. These infections can run the range of being pretty mild, or even killing the bird. Unfortunately, you may be dealing with something that may not go away. Did you just get new birds? I would isolate the sick rooster as soon as you can anyway. If you want to try treating him while you try to figure out what is going on, you can go to the farm store and get Tylan 50 in the goat/cattle section. Ask for some small needles and syringes too. If he is a large fowl (not small or bantam) give 0.5 (1/2) of a cc(same as ml) injected in the back of the neck under the skin. Have someone hold him, pull up some neck skin and slide it under the skin. Don't stick yourself on the other side! Do this for 5-7 days. Baytril is even better if you can get it from your veterinarian.
You have some tough decisions to make. If you are only keeping chickens for pets, some of these conditions can be managed with a closed flock or even vaccinating. If you were wanting to sell birds or hatching eggs, you will possibly get someone elses's flock sick. Many people, with far more experience than I have, would encourage you to cull a bird showing these symptoms. These are people who I think count on being able to sell chicks and eggs. They cannot have a sick bird passing something around. This may be the only foolproof way to deal with it.
If the bird dies, keep it cold(not frozen) , and contact your state veterinarian. Just google for a contact. You can take the bird in for testing and find out what made it sick. This can be very important in helping you decide what to do. I would call and talk to someone even if the bird does not die. They can be very helpful. Some states offer this service for FREE! Some are low cost. I did hear that at least one state (I think NY) was expensive.
So I hope the above is helpful. These things are confusing and difficult. Good luck and keep us posted.