It needs cleaning but as you say, some areas are eternally covered in poop. Chickens poop a lot wherever they are, that’s just what they do. Usually they are moving around so it doesn’t build up that much but at night they are roosting and not moving around so it builds up. Poop management is always an issue, especially under the roosts, but you do not need to keep it as clean as your bathroom. Some chicken poop or chicken poop stain is not going to hurt anything. Don’t set unrealistic expectations for how clean it has to be, you’ll work yourself to death and come to hate the chickens.
The test for how much poop is too much is smell. If it stinks you should have cleaned it out earlier. Wet poop is the culprit, wet poop breaks down with anaerobic activity and can really stink. The poop can get wet from the weather, from waterers, or just from fresh poop building up thick enough that it doesn’t dry out. That’s why the area under the roosts can be so critical. It can really build up there and stay wet.
That is a great size for nine chickens. I’m not sure if the 10’ x 18’ includes the run or not, but that is a huge amount of room in the coop just from the pictures. As long as the coop floor doesn’t get wet you can probably add some bedding of some type and probably never have to clean it out for a year except under the roosts. The other poop should be spread out that much. As long as it is dry, you are in great shape. Having the door open out which is probably the easiest thing to do is a great idea. If you were building new raising the door so it is always above the bedding is an easy way to manage this but you probably don’t have that option.
Where are the chickens roosting now, on the roosts or in the nests? The reason you want the roosts higher than the nests when you are building the coop is that the chickens tend to roost on the highest thing available and you don’t want them to sleep in your nests. They poop a lot at night and you don’t want poopy eggs. But the key is that they might might might sleep in the nests, not that they absolutely will. If your chickens are sleeping on the roosts and not in the nests, you do not have an emergency. You don’t have a problems that has to be fixed right now. Life is actually good the way it is. If you ever add new chickens it would be good to have the nests lower than the roosts for sure, there is a reasonable chance the new chickens would sleep in the nests for a while. But if they are sleeping on the roosts don’t stress yourself over a problem that does not exist.
I put my juvenile roost over my nests. When I integrate the young chicks sleep there until they move to the main roosts. I use the top of my nests as a droppings board. Even if the chickens are sleeping on top of the nests and leaving poop on top of the nests, you do not have a problem as long as the inside of the nests where the eggs are stays clean. Don’t go looking for problems that don’t exist.
I’m not sure why you are that concerned about the stones in the run? They are rounded off, not sharp, so the chicken swill not hurt themselves scratching on them. They might be hard for you to walk on, you might twist an ankle.
A muddy run can be a problem. They poop out there too and if it gets wet it can smell. You might read through this to see if you can get some ideas to fix it. Sometimes when it sets in wet there just isn’t a lot you can do. Even if you cover it rain will blow in from the side.
Pat’s Big Ol' Mud Page (fixing muddy runs):
https://www.backyardchickens.com/web/viewblog.php?id=1642-fix-a-muddy-run
One thing you do not want to do is change the drainage so water runs into the coop. That is huge. Is the run where you are planning on adding the sand? If you can build the run up so water drains off of it to other lower areas you can do yourself a lot of good. If the area is low so water stands in it, just adding sand won’t really help, the water will stay there under the sand. When I built my coop I hauled in some dirt to raise the floor level enough so water doesn’t run in, then put the bedding down. It stays dry. Wet is your enemy as far as smell goes, whether in the coop or in the run.
I don’t have a clue what is going on with that hen that doesn’t want to get down from the roosts. Is that the one you show on the roost so she is not a Silkie that cannot fly? She has plenty of room to spread her wings and fly down, which is what mine do off of the 5’ high roosts. Is one of her wings hurt? You might look at her wing flight feathers to see if they have been clipped.
Those are not what we call ladder roosts. A ladder roost is like a ladder leaned against the coop wall. This link should give you some photos. If you decide to build a roost like this to help that hen, 12” up and 12” out is a general recommendation on dimensions.
https://www.google.com/search?q=lad...=MorFV6OFGYnSmwGRj5HIDA#imgrc=Q9vcTbpyh86jKM:
If you must rebuild everything in there, the way I determine height is to figure out where the top of the bedding will be, then set the nests. Some people are really happy with nests on the floor, others like them raised up higher so they don’t have to bend as much to get the eggs. Then make the roosts higher than the nests. Usually a foot higher than the top of the nests is good.
Looking at your next to last photo that shows the nests, you might cut those nests off if you can’t remove them and put a flat piece of plywood to cover that so poop does not drop through and put the nests on that lower shelf. That way you could leave your roosts as they are.
You have a tremendous amount of room in there which gives you a lot of flexibility to do things. There are just so many different ways you can do any of this. Yes, it needed to be cleaned out but people often care a lot more about most of these things than the chickens do. As far as I am concerned what your chickens really need to stay healthy is clean water appropriate food, and a dry place to stay. A little poop isn’t going to hurt them as long as it is dry.
I agree chicken TV is often better than anything on cable, satellite, or antenna. They are fun to have and fun to watch. Plus they give you eggs. With room like that they don’t have to be a lot of work either, maybe do something with poop that builds up under the roosts and clean the rest once a year. Just don’t set your expectations too high as to how clean it has to be.
Good luck and welcome to the adventure.