Family Tree Project researching family history

For years, my cousin Christine and I had not been able to get very far researching the family history of our great grandmother. We couldn't find Mary Ann's birth certificate. There was a family story that she had been adopted. 

Objectives with the genealogy task ahead-

1/ Find out whether she had been adopted. 

2/ Find her birth certificate

3/ Research more on her ancestry and parents. 

4/ Find out about her brother Andrew and his family history. 

After a visit to the Public Record Office, this is what we found. .......................

Looking through old Argus newspapers, we found an article about her parents. Her parents Bridget Brogan and Andrew Byrne, along with Bridget's brother James were thieves in Melbourne and sent to jail for a few months in 1874 for stealing. Mary Ann would have been born while Bridget was in Old Melbourne Jail, so that was probably why we couldn't find her birth certificate. 

Next we looked through criminal trials and found details of their jail sentences. This confirmed that Mary Ann's mother was in Old Melbourne Gaol. 

Next we looked through childrens' home papers. Andrew junior and Mary Ann were removed from their mother when Andrew was 4 and Mary Ann was 2. They were neglected children and their father had deserted the family. They were sent to The Royal Parade Industrial School in North Melbourne. They were both fostered by Catherine and Michael McCarthy from Fitzroy. 

When Mary Ann was 18, she finished at Reformatory School. 

Mary Ann married Henry Thomas Stack when she was 22 and had 12 children. 

Andrew junior, was born in 1873 in Epping. He married Elsie Byrne (no relative) in 1902 and they had a child Violet Verna. He was 40 when he divorced Elsie in 1913. Mary Ann ended up being guardian of Violet. In 1915 Andrew enlisted in the army from Perth. He saw service in France. He sadly died in 1922 in Queensland. Violet had no children as far as we can find out. 

My nana, Alma was one of the 3 girls out of the 12 children. She died in 1949 in Thornbury Aged 74. My grandparents were able to buy her house and lived in it until 1972.

Further research needed:

Where did Mary's Ann's parents go? Did Andrew senior go to Queensland where his son died? When did they die? Where are they buried?