I am definitely going to second the suggestion of dlhunicorn. She has left her body behind, and it is truly best to know what is going on, especially since it has the likelihood of being infectious.
Please, Please consider seriously an autopsy.
P.S. If you need any help identifying or understanding the internal organs, please do not hesitate to ask me and others on the list.
I am a Histologist by trade and have performed and assisted in many veterinarian and human autopsies.
Take care and warmest wishes for your heart to mend, and for your flock to heal.