What is the ruling of Sharia on unregistered marriage in Jordan?
All perfect praise be to Allah the Lord of the Worlds. May His peace and blessings be upon our Prophet Mohammad and upon all his family and companions.
Aishah narrated that the Messenger of Allah said: "Whichever woman married without the permission of her Wali her marriage is invalid, her marriage is invalid, her marriage is invalid. If he entered into her, then the Mahr is for her in lieu of what he enjoyed from her private part. If they disagree, then the Sultan is the Wali for one who has no Wali." [At-Tirmithi, Hadith No.1102]. The Prophet (PBUH) also said: "There is no marriage without a guardian and two honorable witnesses." Related in [Al-Mo`jam Al-Basit for At-Tabarani, pp.6366]. Registration of the marriage contract at Islamic court is necessary for the preservation of rights and failing to do so is punishable by Jordanian Law. And Allah The Almighty 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.
What is permissible for the husband to do as far as having sex with his wife is concerned?
The couple are free to enjoy each other sexually provided that they don`t do it during menses. It is also forbidden for the husband to enjoy the wife from her anus.
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.