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 for the father to give the Zakat of his money to his poor married son?
It is permissible for the father to give part of the Zakat to his poor son, if the latter was sound and healthy, because in this case the father isn't obliged to spend on his young son, even though; he is considered one of the Muslims poor. And Allah Knows Best.
Is it permissible to offer an absentee funeral prayer?
Yes, it is permissible to offer an absentee funeral prayer.
Is Making up Missed Obligatory Prayers an Obligation?
All perfect praise be to Allah, The Lord of The Worlds, and may His peace and blessings be upon our Prophet Muhammad and upon all of his family and companions.
Missed obligatory prayer/prayers is a debt upon Muslim and making it up is an obligation, since the Prophet (PBUH) said: "pay the debt due to God, for it is the one which most deserves to be paid." [Agreed upon]. And Allah Knows Best.