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 woman to offer the obligatory prayer after Adhaan (call for prayer), and before Iqamah (The announcement that the prayer is about to begin) in the mosque?
Yes, it is permissible for a woman to offer the obligatory prayer immediately after the Adhan and before the Iqamah in the mosque. And Allah Knows Best.
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.
Is it enough to say Tasbeeh (Saying Subhaana Rabbiya Al-‘Atheem during Rukoo`, and saying Subhaana Rabbiya Al-A‘laa during Sujood ) once, or twice during Rukoo`(Bowing in prayer) and Sujood (Prostration)?
All perfect praise be to Allah, The Lord of The Worlds Yes, saying Tasbeeh once during Rukoo` and Sujood is enough, provided that the worshiper`s attentiveness of the heart isn`t undermined during each. As regards the recompense, it depends on the number of Tasbeeh. And Allah Knows Best.