I just finished reading this thread and it seems to me that if it were botulism she wouldn't be living by now or eating, drinking, and communicating. How is her poop looking?
Do you only have 2 ducks? 1 drake and her? If that is so I'm leaning toward over-mating. Which could explain the eye problem too. Sometimes the drakes will go for the eyes. He also could have hurt her back or legs if he was too rambunctious.
Whatever you find with her vent I would still get some calcium Gluconate at TSC and give her 1ml orally making sure that you get it down the DUCK'S RIGHT side of her mouth otherwise it goes down her trachea. It's only about $8 I think and you need to have it on hand anyway.
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