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.
What is the Islamic ruling on adoption, and what is the legal window through which a person can be kind to an orphan girl, attend to her needs and raise her as his own?
Kindness to an orphan entails a great reward from Allah, but adoption is prohibited and invalid. Therefore, it is permissible for the aforementioned person (for example) to make his brother`s wife breastfeed that girl so that he becomes her uncle by suckling provided that he informs her that she isn`t his biological daughter.
Is it permissible to swear by (Allah "The Living")?
Yes, it is permissible because "The Living" is one of Allah`s Attributes.
Is supplicating in Qunoot, at times of affliction, during obligatory and voluntary prayer a Sunnah, and should it be done before Rukoo` (bowing), or after it?
At times of affliction, it is a Sunnah that Muslims supplicate in Qunoot after the final Rukoo` of each obligatory, or voluntary prayer as individuals, or in congregation.