I would leave the bio-filter and just clean the prefilter every week. I use a long handled swimming pool leaf skimmer (about $10 at walmart) to remove debris from the bottom every week. Works like a charm and only takes minutes.

Since your pond is accumulating sludge on the sides and bottom you could dredge the bottom with a leaf skimmer or fine mesh net, take a garden hose to the shelves (not to strong of a flow- you want to keep the fuzzy algea on them), then do a partial water change, taking water from the bottom of the pond, and then clean your prefilter pads a couple times during the week. You will be stirring things up so that is why you will need to rinse the filter pads.

Happy ponding.