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.
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.
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.
What is the ruling on not offering prayer in a nearby mosque, and going to a distant one?
All perfect praise be to Allah the Lord of the Worlds. May Allah`s peace and blessings be upon our Prophet Mohammad and upon all his family and companions.
Praying in the nearby mosque takes precedence unless there was a circle of knowledge, or a larger congregation in the distant mosque provided that the congregational prayer in the nearby mosque isn`t undermined. And Allah Knows Best.