Starting over with the ducks would be a good idea. Once they pick up this type of habit it's hard to stop it. Muscovy generally are easy going. They do occasionally fight for dominance so perhaps that what started it all. You may never know the real reason.It is definitely the ducks starting it. For some reason this flock of ducks was very aggressive, and I have had issues with them chasing the chickens in order to pluck and eat their feathers, and unfortunately it has escalated to this. Whereas, I have not seen the hens fighting/picking on each other basically at all. The hens all seem very docile.
I will definitely work on improving their diet and increasing protein, and then maybe I will introduce some new ducklings to the flock in the spring.
I really appreciate the insight and advice.