Chambers, after re-reading your thread, I'm betting the "black mud" is actually some charcoal from the original burn piles inseide your pond...it's no harm. The "string looking particles" are almost certainly a species of Filamentous Algae. FA grows on the bottom, or can be loose filaments. "Mat Algae" has just pulled loose from the bottom due to trapped air bubbles lifting it.

You said your water started as "Clear", but only had 10-12 inches of clarity...I would not consider that clear. IF you do in fact have suspended clay, you can still get a green tint to the water due to a planktonic algae bloom growing in only the upper few inches of water.

Have you done a "Jar test"??? If not, get a couple quart canning jars and gather one sample from a couple feet deep, and one from the upper part of the water. Put on lids and let them set, undisturbed for a few days and see if anything settles out, and if the water clears up completely. If it does not clear, but has some sediment on the bottom, but a green tint still, put the water in a dark place, like a closed closet for another few days and see if it clears. If it does, you have an algae bloom (a good thing), but the sediment was colloidal clay (a bad thing). If little or nothing at all settles, go to a grocery store spice aisle that carries "McCormick" spices, and get a small jar of Alum (stocked alphabetically) and spinkle in 1/4 tsp and shake.....if it is clay suspended, the water will turn crystal clear in several hours when again, left undisturbed.