What is the ruling on working for a company that manufactures cigarettes?
All Perfect Praise is due to Allah, The Lord of The Worlds
Working for a company that manufactures cigarettes is forbidden because smoking itself is forbidden, so its production, selling and circulation are forbidden as a result since they aid in committing sin, and whoever aids in that is like the sinner himself. And Allah Knows Best.
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 it permissible to offer Istikhara prayer (seeking guidance) after Witr Prayer (A confirmed Sunnah which is offered after Isha prayer and before Fajir prayer with a minimum of 3 Rak`as and a maximum of 11)?
It is permissible to offer Istikhara before and after Witr prayer as it is permissible at any time except that in which prayer is disliked. And Allah Knows Best.
What is the ruling on having a second congregational prayer in the mosque?
All perfect praise be to Allah, The Lord of The Worlds, and may His peace and blessings be upon our Prophet Muhammad and upon all of his family and companions It is disliked to have a second congregational prayer in the mosque which isn`t visited by travelers like the neighborhood`s mosque, and which has an appointed Imam, save with the latter`s permission. Nevertheless, if the mosque is visited by travelers, it is permissible to have a second and a third congregational prayer, whether it has an appointed Imam or not, or whether he permits that or not. And Allah Knows Best.