Hands on hatching and help

I have a chick that was malpositioned with legs above head. As I was assisting and saw that the yolk had not been completely absorbed. I put the chick in a cup with half of its shell still on. Do I keep her in the cup in the incubator or take her out and but her in the brooder. She is really trying to get out of the shell while she is in the cup. She is one unhappy chick. Please help.
 
You keep her in the incubator. Are you certain it's yolk and not just leftover gunk (embryonic waste)? Yolk will be bright yellow.
It look yellow, but I did not go further with taking the rest of the shell off so I am not sure. Once I saw that there was still stuff there I stopped and got on here. She is really trying to get out of the egg while in the cup. Should I take off the rest of the shell or just leave her in it. Thank you so much for your help.
 
If it is yolk do I just keep her in the bottom half of her shell like she is right now.
 
It looks like it is her intestines. There is a whole that is not closed. Now what. If anything. She came out when I shinned the light down.
It may just be the "umbilical" cord hasn't dried and separated. In which case, it's not a problem if it isn't real thick. A pic would help us help you.
 

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