To the original poster...
One thing that might take care of more than one of your worries is using USDA Food Grade Diatomaceous Earth (DE) in the coop, outside runs, in the food, and on the birds themselves. (ONLY use food grade DE, NOT the DE sold at pool supply stores.)
DE has multiople uses. One, by continually mixing in DE with the birds feed in a mix of 5% DE to 95% feed will rid the birds of all intestinal parasites and worms. It is very helpful to always do this, because it will rid the birds of worms that travel between the luns and intestinal tract, and their larvae and eggs as well as all other intestinal parasites. It also provides a source of silica in their diet which will help them grow cartilae, strong joints, beaks, and toes.
Dust the birds with the DE to rid them of all external parasites, including fleas, ticks, and mites. Make sure to rub the DE in good, all of the way to the skin. Give them a tub of DE mixed 50/50 with play sand (bought inexpensively at Home Depot or Lowes) to allow themselves to dust bathe in it.
Sprinkle DE liberally throughout the nesting boxes and the coop, including over any bedding to rid the areas of all bugs like mites, plus the DE acts as a deodorizer as well. It helps kill the smell of the ammonia and chicken poo, both inside and out.
Use the DE liberally like suggested above and change out the bedding or clean out the coop regularly and compost the poo and you should have little to no problems with the smells you are afraid of.