I agree that lots of cow poo may cause more problems than it will fix. There may be long term bacterial and water quality problems but I am not sure.
Although, I do use a small amount to fertilise my pond before fry season.
The higher you can keep the water level in your pond when you do try out the airstones and new bentonite the higher it will seal.
It probably wouldn't hurt to turn on your air pump now anyway and run it. The current should still keep some bentonite in suspension and it may help seal any seepage below the water line over winter.
If that works then you only have to worry about the rest next Spring.
If you can get a long wooden ladder and leave it in the pond at one end it will make sure you are safe to get out of the pond when you fall in. Not if but when. I've learnt the hard way.
It won't hurt the fish but it'll keep you safe.