Hi, I'd leave the run dirt.. unless it rains every day or at least every other day, it shouldn't be a problem, I've had mine knock over their auto waterer drained a 2500 gallon water tank (we are water haul), so the results of that was a mud bog that I sank up to the tops of my sneakers. I'm confused about a couple of things, how is the floor of the coop dirt when it's sitting at such a angle.. and can you figure out why on earth all that lattice? personally? I'd remove all of that and open it up.