Is the one who doesn`t offer prostration of recitation during Quranic recital considered sinful?

Prostration of Quranic recital is a Sunnah due on whosoever recites a verse that contains a prostration. It is also a Sunnah for the reader and the listener. However, none of them is considered sinful for not offering it, but they deprive themselves from a great reward. It is obligatory to offer the prostration of Quranic recital in congregational prayer following the lead of the Imam.

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 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.

 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.