Sometimes starting over isn't so bad. I'm not sure where you are located or how fast your pond refills. If up north and plenty of water, is there any chance you could siphon the pond down low in winter, let a winter kill mostly resolve the issue, and then use some rotenone to finish them off or even seine it while the water is very low? That lowered water level might also give you the opportunity to add structure, contours, and anything else you'd like. For restocking, you could go heavy on the forage first so the fish you stock grow fast.
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