Shellie, there are a few things you have to keep in mind:
1. Microbes that eat the muck, will also eat your fish, of course, after killing your fish first through a painful death. Just a warning. The only way to remove the muck is manual approach. Then control the sources that create the muck. When you are ready to proceed to remove the muck, there are various methods that I can offer you to protect your fish, while removing the muck manually. Lots and lots of work.
2. I'll bow out on this one. My knowledge on aeration system is extremely limited when it comes to small ponds. I only work with the local agencies in dealing with 10 acres and larger lakes.
3. Once the aeration system is, AND, the remaining turbidity settled, which is not long, stocking time!!
