Spicelanebass I suggest you call Bob Lusk at the Pond Boss office. He has experience with lakes like the one you describe.

Shock surveys do have limits but are a good tool . An experienced operator will know how to interpret the data (catch records , shock survey , visual inspection , water analysis etc) to give you a complete picture. Water chemistry and temp have an effect on shock surveys but can be managed around.

GS can be a problem and there are threads here on the topic.