I took a car from the Orphans' Fund Development Institution; is there usury (Riba) involved in this transaction?

If the Sharia's conditions were met, then there is no harm in this. And Allah The Exalted Knows Best.

Is it permissible for a woman to conclude her marriage without the approval of her family?

No marriage is permissible without the presence of a guardian and two trust worthy witnesses, and the woman whose family had denied her right in getting married to a God-fearing, financially and physically capable man should go to the court.

How should I be kind to my atheist father?

Allah, The Exalted, has decreed and ordained his slaves to be kind with parents, even if they are polytheists, by honoring and obeying them in all that isn`t sinful, so that they might love Islam and embrace it as a result.

Does the deceased hear the supplications or recitations of those visiting his/her grave? And does making constant supplications for the deceased who didn`t adhere to performing the prescribed prayers ameliorate his/her affliction?

Praise be to Allah the Lord of the Worlds.

In principle, the dead hear the living since it has been rigorously authenticated that the Prophet (PBUH) ordered the bodies of the idolaters slain in the Battle of Badr to be buried. He then approached them and called them one by one and said: "Have you found what your Lord promised to be true for we have found what our Lord promised us to be true." Umar asked him: "O messenger of God! Why do you speak to lifeless bodies?" The Prophet (PBUH) replied: "By the One Who has sent me with the truth! You do not hear my words better than they do except that they cannot respond." [Agreed upon].

However, not all the deceased are in the same situation because Allah The Almighty Knows: "Before them is a Partition till the Day they are raised up." [Al-Mu`minun/100]. Moreover, supplication reaches the deceased. And Allah Knows Best..