Good job improving your pond!
If you just cleared the easy muck in the deep spots, would the muck in the shallows eventually works its way down into the deep spots in a few years?
If so, then perhaps you should just clear the deep spots every few years as opposed to doing a "perfect" job now.
OTOH, have you seen a fish kill when you stirred up all of the muck this time? (I believe you were previously not sure of the fish population in your pond.) If your pumping project causes a fish kill every time you perform it, then obviously you can only use that method in the future when you are planning on a new fishery.
It sounds like you have already performed an impressive amount of labor. Good luck on getting your pond back into tip top shape!
