JMayer, just a quick point on the muck from the bottom of the pond....
The jury is out, so to speak, on whether or not that muck is of good value as soil, if I recall correctly.
You may be able to get some reduction in the organic muck by either adding aeration or muck-reducing bacteria or microbes. Regarding the bacteria or microbes, a concern could be if you have too much flow-through water. I'm not sure that's the case though.
