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 permissible to include a will requesting that a Holy Qur'an buried along with me?

It is not permissible to include a will requesting that a Quran be buried with the deceased in their grave. This is because the body of the deceased typically decomposes and may release impure substances, and it is not allowed to expose the Quran to impurity. Intentionally desecrating the Quran is an act of disbelief. Instead, read the Quran during your lifetime, as it will benefit you after death. And Allah Knows Best.

Is it permissible for a woman who has become pure before the end of forty days of confinement to perform different acts of worship? and is it lawful for her husband to have sex with her?

Once postpartum bleeding ceases and she is certain that it won`t happen again, she becomes pure, and so she should perform Ghusl (ritual bath), pray, and fast. She can also have sex with her husband even before the end of (40) days because the minimum of postpartum bleeding is a moment, and the maximum is (60) days. However, the postpartum bleeding for the majority of women is (40) days, but this does not apply to rest of them.

Is a wife considered divorced if her husband refused to go to bed with her (for sexual intercourse) for two months?

A wife doesn`t get divorced no matter for how long her husband refuses to have sex with her, and she had better go to court.