Is it permissible for a person to sever ties with his sister because her husband had quit prayer and done him harm?
A sister is a blood-relative and maintaining blood-relations is obligatory in Islam. As regards her husband, he should be invited to the way of Allah with wisdom and beautiful preaching.
My husband told me that he concluded our marriage with a fake name that belongs to another person, because he was sentenced. Nowadays, he recieved an ID, passport and birth certificate with the his current name. What is the ruling on being married to him?
Praise be to Allah, The Lord of The Worlds, and may His peace and blessings be upon our Prophet Muhammad and upon all of his family and companions. As regards being married to the person mentioned in your question: The marriage is valid so long as he was the same person your guardian concluded the marriage with, even if he changed his name i.e. if your marriage contract was concluded with the same person, since what counts regarding marriage is the persons not names. And Allah Knows Best.
Is it permissible for me to make up for my late father`s missed fasts? and should I make an intention to this end by saying: "I intend to make up for my late father`s missed fasts?
It is permissible to fast on behalf of the deceased father in order to make up for his missed fasts, and you should make the intention for offering fast from night time, but uttering the intention isn`t a condition. And Allah Knows Best.
Is Zakah due on the orphan`s money?
Yes, Zakah is due on the money of the orphan.