Multipronged absolute disaster

[centrarchid]

Pictures needed.

I did not catch what and how you are feeding them. You did mention red food coloring possibly in feces coming from food.

 

[fat marans]

...gaps you forget to mention.

Oops, I thought I mentioned them. Some of them are in post #1 above. I will take photos when convenient, sorry.

 

[centrarchid]

I am going to be direct and say you are not providing useful information so far.

 

[Wyorp Rock]

I am going to be direct and say you are not providing useful information so far.

Agreed.

You will get bombarded with a lot questions...I'm sure it's overwhelming, but I can't stress how useful more information will be.

@centrarchid can probably show you some good examples of how to make separation pens/housing to get them to a cleaner environment, but the more info you provide the better we can help you.

 

[ChocolateMouse]

If you can get the area clean properly I would just stick them back where they were.
Again, you can prevent dropping buildups with deep litter. I will *ahem* break it down for you. (That was a composting pun.) Step by step.
Some science on how it works first;
Chicken poop is dangerous because of parasite loads and high ammonia levels. Ammonia levels cause the smell.
Ammonia is made up of nitrogen and hydrogen. There's a specific set of bacteria that needs nitrogen and carbon to grow. The bacteria are basically capable of consuming the nitrogen and leaving hydrogen behind. Hydrogen on it's own combines with oxygen in the air and becomes harmless water. If you mix carbons together with sources high in nitrogen (chicken poop) the bacteria will naturally break down the ammonia in the chicken poop, binding the nitrogen to carbons and creating wonderful rich garden soil. This is also an ideal environment for bugs, especially earthworms.
Wood chips, leaf litter, shredded paper, sawdust, straw, pine shavings, etc are all high carbon sources. But wood chips work best for chickens. Avoid cedar.
Danger two is parasites. But SOME parasite loads are normal and harmless. The goal is to prevent the chickens from walking in/pecking at/eating the parasites they shed. The healthy soil environment provided by the waste breakdown by the bacteria will also provide a home for things like mites, insects and tardigrades that eat chicken parasites of all sizes. Some of them will still live, but many of them will get consumed by the hostile environment.
Those insects then encourage the chickens to dig through the litter to find and eat them, thereby burying their own waste and spreading it throughout the deep litter allowing more surface area for beneficial bacteria and insects to consume the chicken waste.

So, tl;dr deep litter works by providing a rich carbon source that (through micro-organisms) breaks down chicken poop and provides a home for insects that eat chicken parasites.

So to use deep litter;
First making sure you have enough space. Too many chickens in a too small a space will be impossible to control the waste without removing it somehow and stressing out your birds. 10 sqft (about 3.5'x3.5') per bird is a good size to aim for.
Then remove any chicken waste that you immediately can. A rake is good for this.
Fill the chicken pen with about one foot of wood chips. Any kind of wood chips except for cedar is fine. You can probably get them for free from local tree companies.
Every day, throw a little scratch grain on the wood chips to encourage them to scratch around and mix it up.
If you follow these steps it will help control your waste.
You can use a similar technique inside the coop, but need only 4sqft of coop space per bird (assuming they have regular access to the outdoor pen).
To clean the inside of the coop, scoop out all the old bedding and poop, scrape poop off of walls/roosts/etc, sweep it out with a broom, hose it out, and then spray everything with a solution of 1tbsp bleach to 1 gallon of water. Allow it to air dry for a few days with all the doors open.

For cleaning them off, I would soak them in a little bit of soapy water. Dish soap should work well. Use a pair of scissors to cut nay feathers that have poop stuck on them.

Check their feet for bumblefoot.
https://www.backyardchickens.com/articles/bumblefoot-in-your-flock.65979/
https://www.backyardchickencoops.com.au/Signs-Symptoms-And-Treatments-For-Bumblefoot-In-Chickens
https://www.tillysnest.com/2015/12/non-surgical-bumblefoot-treatment-html/

Check their legs for lifted or damaged scales that could indicate leg mites.
https://www.tillysnest.com/2012/04/scaly-leg-mites-html/

Look over their vents and see if they have any of these problems;
https://www.backyardchickens.com/articles/vent-gleet-aka-nasty-chicken-butt.64647/
https://www.tillysnest.com/2012/12/vent-gleet-prevention-and-treatment-html/
http://www.the-chicken-chick.com/2012/04/prolapse-vent-causes-treatment-graphic.html
https://www.mypetchicken.com/backyard-chickens/chicken-help/Vent-prolapse-overview-H263.aspx

If they do have anything, treat appropriately.

Then make sure they are on a healthy diet of high quality feed to help them have healthy poops. Make sure their water is clean and put a little bit of unpastuerized apple cider vinegar or probiotics in their water to help them with maintaining healthy gut flora. I use Probios brand probiotics.

I think that will probably give you a good start to getting them clean and healthy again.