Is it permissible to listen to chants praising the Prophet if accompanied by musical instruments?
If singing, or chanting in praise of the Prophet was accompanied by a forbidden musical instrument, then it is forbidden.
Is it permissible to fast on behalf of the dead who died owing missed fast to make up?
His relative should fast on his behalf, and it is permissible for the guardians to give permission to non-relatives of the dead to fast on his behalf as well. And Allah Knows Best.
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.
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.