I`m a pious Muslim woman, but my husband isn`t, what should I do?
You should exercise patience, make supplication that Allah guides him to the straight path, and keep advising him kindly.
Is it permissible for a woman to say that she loves her husband more than her father?
It is impermissible for her to say so since this would hurt her father deep down. Allah, The Almighty, Says in this regard (What means): "And that ye be kind to parents." [Al-Isra/23]. Saying such a thing to her father isn`t an act of kindness since she should keep it to herself even if she felt that way.
Is it permissible for one to shake hands with his uncle`s daughter?
No, it isn`t because he is a non-Mahram (Marriageable) to her.
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.