After I added more chips today, I walked around the coop and only noticed the death smell in one spot. Turns out, it wasn't my coop or run, it was a fly trap! Awful smell. And, when I went to take it down the bag split! So gross. The flies are gone now with the chips but before they were around with the dirt. Our run is 400 sq ft with 10 chickens, so it will take me a little while to get the chips where I want them. Thank you all for your advice. I'm going to keep adding the chips daily until I get to about 6-8 inches.