You are going to be spending a significant amount of money on your restoration project, just by virtue of its large size.
Is there any chance of constructing a sediment/retention pond between the two existing large ponds?
If you were able to build it with a large freeboard, then you might be able to effectively screen the outflow pipe to at least exclude sizeable "undesirable" fish from the neighbors. A healthy population in your lake could then hopefully deal with the fry that come through.
Hard to justify the expense for that alone, but any silt and muck caught in that sediment pond would be adding to the life of your large pond.
