Agree that pics would be helpful. Poop boards installation to me meant freedom from deep- litter issues. So you have both going on though? I use white vinegar in my coop for cleaning. I also have white vinegar in mason jars with orange and lemon rind. After a few months it's great to clean with that as it leaves a citrus smell instead of pickle smell

I'm sure you can get the rat issue solved by first eliminating the rats, then putting control plans in place like getting rid of anything that is attractive to them - bedding, poo and feed. Personally I would not put rat poo in my garden but I would certainly spread it under trees and landscaping as mulch.