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 for me to make up for my late father`s missed fasts? and should I make an intention to this end by saying: "I intend to make up for my late father`s missed fasts?

It is permissible to fast on behalf of the deceased father in order to make up for his missed fasts, and you should make the intention for offering fast from night time, but uttering the intention isn`t a condition. And Allah Knows Best.

Is it permissible to make up missed prayers at the times in which praying is disliked?

All perfect praise be to Allah,The Lord of The Worlds                                                                                                                                                                        It is permissible to make up missed prayers at any time even that in which praying is disliked. Absolute supererogatory prayer is forbidden to be performed at the times in which praying is disliked, and this also applies to Ihram and Istikhara prayers. However, there is no harm in offering prayers in Mekah during those times. And Allah Knows Best.

What is the ruling on someone who perform their prayer after finishing it because they believe they missed a Rak'a, a prostration, or that they did not perform it correctly (thinking their prayer was invalid)?