Is it permissible to pay the Zakah to my grandmother who lives alone in a rented accommodation with bad conditions noting she had three sons.
Zakah cannot be given to ascendants (parents and grandparents). It is obligatory for her sons and grandsons to provide for her, and they would be sinful if they fail to do so. And Allah Knows Best.
Is Zakah due on the orphan`s money?
Yes, Zakah is due on the money of the orphan.
Is it permissible for me to make up for my late father`s missed fasts? and should I make an intention to this end by saying: "I intend to make up for my late father`s missed fasts?
It is permissible to fast on behalf of the deceased father in order to make up for his missed fasts, and you should make the intention for offering fast from night time, but uttering the intention isn`t a condition. And Allah Knows Best.
What is the ruling on reciting verses of the Holy Quran on water, then drinking it?
It is permissible to recite Quran on water, then drink it as a kind of treatment since the Quran heals. Allah, The Almighty, Says (What means): "We send down (stage by stage) in the Qur’an that which is a healing and a mercy to those who believe: to the unjust it causes nothing but loss after loss." [Al-Isra`/82].