You might need to think about starting over with the big pond. Bill Cody recently posted about the life cycle of a pond. Yours appears to maybe fit a lot of the things he was lecturing about. I don't remember where the post was but I'd definitely look for it. If Bill says it, I believe it.

One thing you might need to be careful of. You mention that the smaller pond has a shale bottom. If you deepen the bigger pond, is there a chance that you might dig thru a shale bottom and have a real problem? I don't know anything about shale.