How big is the run? Would it be cost effective to put in stone? I've heard you can get bags of it at Walmart for a couple of bucks. My run was manky and muddy and stinky, and I used the stones from under our old deck. It seemed to help!
I used to have gravel mixed in but it's all disappeared now... I've been thinking about buying a couple more bags. when you say stone how big are you talking?
I noticed that when it doesnt rain for a while then rains and you dig it up it smells the worst. When its dry its not so bad. I try not to mess with mine if it has been raining a lot. Once it dries out I go in with a garden hoe and till it up.
I put a tarp over my outside run. That helps alot. The birds like it too. They stay out in the rain. I give them fresh hay everyday to pick at and dig in. That keeps it dry. When it gets to stinken I fork out all the old hay, put down pine chips and some new hay. I have to stay ahead of it because I have a deck close by and nobody wants to be overcome with the smellies!
We have a product in Maryland called Leaf-Gro (leaves collected from residences and then composted with nothing added). I added a few inches in their run and oh my goodness, what a difference. It literally doesn't smell at all, AT ALL. We have compacted clay dirt and no matter how many times I tilled, pitchforked, raked, I couldn't manage the smell. It wasn't horrible or terrible or awful mind you, but I didn't like the smell I was smelling. And I really wanted to nip it in the bud. So far so good.