WOW lots to think about here.
The pond that is now muddy had the difussers in 5 gallons buckets so it is not stirring up clay off the bottom. I will turn the diffusers off and see if that helps. The second pond I mentions does not have diffusers and stays clear and it does not get allot of wind on it as it is protected by the big ponds dam.

I did not stock bullhead but I know there are bullhead in the pond because I have caught them before. So should I kill all the fish out and start over?

Also the wind does hit the face of the pond dam very hard and causes errosion. Should I rip rap the face of the dam?

I'm just at a loss. I will take it one step at a time until I figure it out.