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 a young man and a young woman to enter into a covenant as a married couple without having a true seclusion (Khalwah) until their marriage contract is officially concluded?
The relation which isn`t based on a marriage contract is forbidden, and entering into a covenant as a married couple is unaccounted for and is from the evil suggestions of the devil.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
Is it permissible for a praying person to make supplication in each Sajdah (a prostration) of obligatory prayer?
It is permissible for a praying person, whether praying individually, or in congregation, to make supplication during Sujood (prostration) in obligatory, or voluntary prayers. However, it is disliked for the Imam to do so since he is required to spare the prayer performers any sort of hardship, unless he is leading a certain group who don`t mind him extending the prayer.