Dennis--
What a frustrating situation. First, a question--you don't mention aeration; are you doing it? Second, you have a shallow-enough pond that the water temp is undoubtedly high and facilitating algal growth. As to the Crystal Plex not working, it is very similar to Cutrine Plus--also a chelated copper product--and so it certainly should. Are you applying the algaecide by spraying it, or just dumping it in? Certainly, the muddy look you describe is not healthy, thriving algae but sounds like the muck which results from algae you've killed. After I've used Cutrine, I paddle around with a kayak, splashing and vigorously paddling to break up the clumps of algae. The
chara will be affected by the muck, as well as the chelated copper, and so you undoubtedly will have a huge amount of degrading biomass in the pond, which will facilitate regrowth; thus you are right that it makes sense to mechanically remove as much as possible, although what a tough job--you can, however, compost it. If
Biokleer is what was recommended, I wonder what it will do for you as it is more a degreaser than a farm-pond product; you might consider a large does of a more standard farm pond microbe treatment, such as
Aqua-T or a similar product. I also suspect that with the shallow water column using a dye product would be important.
Others may have other thoughts, but it seems to me that the biggest problem you have will be the overall relative shallowness of the pond, which is a tough one to address.
Good luck getting through a tough patch!!