Is it permissible for someone to make a supplication to Allah to marry an already married, or an engaged woman?
No, it isn`t, and the person who does so is sinful before Allah, The Almighty.
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.
I am an author, and I have books stored with me. Is it permissible to pay my zakat in the form of books containing beneficial knowledge for poor students, such as chemistry and mathematics, or religious books that spread Islamic sciences?
Zakat on wealth must be paid in cash from the wealth itself. Therefore, you should pay your zakat in monetary form so that the poor can purchase what they need. 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.