For the smell in the run- things are getting smelly because the poop is just sitting on top of the ground. Break up that packed dirt with a shovel, pitchfork, garden weasel, that garden tool thing that looks like a claw- whatever you can do so that it's not just hard and packed. I like to add all sorts of stuff to my run- I'd try to find leaf litter, some pine shavings, some loose dirt (I get a bag of the cheapest dirt that I can find at home depot and just dump it in), some wood chips, straw (but not too much), sand, really any loose, organic material- put it all in a giant pile and toss on some scratch, they'll spread it out for you. With a loose litter in the run, it allows the bottom layers to compost as things pile up, and the poop to get buried as they naturally scratch around. This is how I have my run and I never clean it, only add more material or mix it around some, and there isn't an issue with smell.