I had a mouse die in the engine of my truck, which I drove everyday. Eventually, you'll be rid of it. In the meantime, get some Vicks Vaporub, and dab it under your nose, and you'll never smell it.
I agree--something died under your coop. Try a couple of bags of Stall-Dry or equivalent. It will help soak up anything..um..wet...and really help dispel the odor. It breaks down very well, and isn't toxic to your birds.