Not much is stirred up since its sucking up all the muck aground the intake so the water is not getting muddy.
I dont think the muck would migrate very quickly even if I pumped out the deep spots.
A really awesome job if you are not making the water too muddy!
My idea for letting the shallow muck "migrate" to your deeper holes was to allow for some wave erosion on the muck while either the weather or you pull down the water level in the pond. Let natural processes work hard for a week (while you take a break) and then pull the water down a few more feet and give it another week to work on an entirely new band of muck.
The wave action should at least work some of the muck down into your deepest water.
I also don't think you need to try to re-establish the original 18-20 foot depth. 12 feet max should be sufficient in your area. Maybe a few deeper holes if you are planning to add some cool-water fish.
You also might try some muck removal in the areas where you have a weed problem and see if adding a little depth there gives you some positive results.
