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 offer Istikhara prayer (seeking guidance) after Witr Prayer (A confirmed Sunnah which is offered after Isha prayer and before Fajir prayer with a minimum of 3 Rak`as and a maximum of 11)?
It is permissible to offer Istikhara before and after Witr prayer as it is permissible at any time except that in which prayer is disliked. And Allah Knows Best.
What should a woman, who has given several births during different months of Ramadhaan, and didn`t make up for them in addition to forgetting the exact number of the days and years in which she had missed fasting, do?
She should make up the missed days of Ramadan after estimating their number, and paying the ransom (in food) due on each missed day that she had delayed making up. In addition, she is obliged to repay the ransom according to the number of years if she was able to fast before that time, but didn`t.
Is it a condition that one should offer two sacrifices for a male newborn?
It is desirable to offer two sheep for a male newborn, and one for a female newborn. Offering one sheep for the male newborn is also permissible as it observes the Prophet`s Sunnah in this regard.