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 to recite the Holy Qur'an or to play a recording at mourning gatherings? Or is it considered an innovation?
Whenever Qur'anic verses are recited, it is obligatory upon everyone to listen, otherwise; they should remain silent. And Allah Knows Best.
What is the ruling on Friday Ghusl (ritual bath)?
Friday Ghusl is a confirmed Sunna (Prophetic tradition) even if a person wasn`t in a state of Janbah (ritual impurity), or physically unclean. However, one who doesn`t make Ghusl on Friday isn`t sinful for the Prophet (PBUH) said: "It is good for a Muslim to make ablution for Friday prayer, but it is better to make Ghusul. [At-Tirmithi & Abu Dawood].
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.