If this is the first time you've noticed the cough, and it ended with the smoke, then I think it was simply smoke related. I would simply keep an eye out for the rooster.
Coughing is not natural in birds. It indicates illness.
Don't confuse stuck food in the crop, however, for a cough. All birds will from time to time get something wedge in their crop and give a bit of a hack to get it up. They make sort of a sharp chirp/squeak. (At least mine do).
If you see any runny nose, bubbling in eyes, wet vent feathers, then you do have illness.
Hard to say on the poo. All chickens have a cecal movement which is thinner than regular poo. That is normal. If it is thin, green, runny, that streaks the feathers, that is not. It could simply be a sign of worms.
So I would not worry but watch to see if this rooster exhibits any more symptoms or if this was a one time thing from smoke. I would also keep an eye out for any other loose stool and consider worming the flock if you haven't done so already.
My thoughts.
LofMc
Poo chart below:
http://www.the-chicken-chick.com/2012/02/whats-scoop-on-chicken-poop-digestive.html