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 the ruling on a person in a state of major impurity (junub) or a menstruating woman (ha'id) reciting the Quran from memory?
It is not permissible for a menstruating woman, a postpartum woman, or a person in a state of major impurity to recite anything from the Quran, whether from memory, from the Quran, from a phone, or a computer. It is also not permissible for them to touch the Quran, based on what was reported from Ali bin Abi Talib that the Prophet (peace be upon him) was not prevented from anything regarding the Quran except major impurity (janabah). (Reported by al-Tirmidhi who said it is a hasan sahih hadith). Menstruation and postpartum bleeding are analogous to major impurity (janabah) as they are all major impurities (hadath akbar).
For those mentioned, it is permissible to mention Allah and supplicate even with verses from the Quran, provided they do not intend them as recitation of the Quran, but intend them as remembrance (dhikr) or supplication (du'a). And Allah the Almighty knows best.
Is the marriage, which lacks a valid legal contract, a guardian, and a court registration, valid?
It is incumbent that a valid marriage contract be concluded in the presence of a guardian and two trustful witnesses, and it should be registered in the court to protect the rights of the wife. Actually, a valid marriage contract is what differentiates between sound marriage and fornication.
Is it permissible to offer prayer at home, or should it be offered in the mosque?
All perfect praise be to Allah, The Lord of The Worlds. It isn`t preferable for the man to pray at home as praying in the mosque is twenty seven times more rewarding. Therefore, this should motivate him to offer prayers in the mosque. And Allah Knows Best.