Your story reminds me of a nervous first time mother!
We all probibly have fatality stories from when we first started raising monarchs. Even now after years of raising them I still feel bad when I lose one, but that is how we live and learn. Newly formed crysalis look a bit deformed and lumpy for several hours, and quite often some of the skin hangs onto the top. It will not hurt anything and eventually will fall off once it dries out. Your best bet is to leave nature take its course and handle them as little as possible especially at first.
As a general rule, if the crysalis looks normal but has crumpled black skin hanging from it just let it be. Only be concerned if it turns black or runny, and in that case remove it and any liquid droppings or debrie and wipe down area with an antibiotic wipe or paper towel with diluted mouthwash on it. Just be careful around other the cats and crysalis.
Take time to look at the photo albums that are posted here as it will give you a better idea of what is normal and abnormal with these little guys.
Hang in there!