What is the ruling on reciting verses from the Qur'an over water, drinking it, and using it to break magic spells, heal illnesses, or burn jinn?
There is no harm on reciting verses of the Holy Qur'an over water and use it for cure. And Allah Knows Best.
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.
When is Istikharah (guidance prayer) Du`a offered, before Tasleem (saying asalamu alikum warahmatu allah wa barakatuh to end the prayer), or after it?
It is offered after Tasleem.
Is it incumbent on the fiancée to obey her fiancé?
When the woman settles in her husband`s house, it is incumbent on him to provide for her and it is incumbent on her to obey him. Before that, and if the marriage contract had been concluded, then she is lawfully his wife and thus she should abide by custom in treating him, but if the marriage contract hadn`t been concluded, then she should treat him as a non-Mahram (Marriageable).