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 supplicating in Qunoot, at times of affliction, during obligatory and voluntary prayer a Sunnah, and should it be done before Rukoo` (bowing), or after it?
At times of affliction, it is a Sunnah that Muslims supplicate in Qunoot after the final Rukoo` of each obligatory, or voluntary prayer as individuals, or in congregation.
My engagement to a young man was announced and blessed by both our families reciting Al-Fatihah. Is it permissible that I take off my Hijab in his presence?
All perfect praise be to Allah the Lord of the Worlds. May His peace and blessings be upon Prophet Mohammad and upon all his family and companions.
Reciting Al-Fatehah (The opening chapter of the holy Qura'n) to declare an engagement isn`t tantamount to a marriage contract and it isn`t permissible for him to see you without hijab or stay in private with you before the conclusion of the marriage contract. And Allah The Almighty Knows Best.
Is the father a Mahram (Non-marriageable) to his son`s mother-in-law?
The father is a non-Mahram (Marriageable) to his son`s mother-in-law, so it is impermissible for them to look at each other, or to have a seclusion (Khalwah).