Someone wiped over his shoes after wearing them in a state of purity, then took them off and prayed without them?
Ablution is not invalidated by taking off leather socks or shoes after wiping over them. However, whoever takes them off after wiping must wash his feet only. If he prayed without washing his feet, he must wash his feet and repeat the prayer. And Allah the Almighty knows best.
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.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
Is it permissible for me to eat from the animal that I slaughtered for Allah to protect my family?
It is permissible to eat from the non-vowed animal sacrifice, and the person is rewarded based on the amount of meat that he had given to the poor. However, there is no evidence in Islamic Sharia indicating that slaughtering an animal protects one`s family, but it is a way for thanking Allah, The Almighty, for his grace.