After I had prayed, I found a drop of menstrual blood and was unsure when that happened; what is the ruling on my prayer and fast?

All praise is due to Allah, peace and blessing be upon the Messenger of Allah.

Your prayer and fast are correct ,and you should not make up for them, and we ask Allah, The Almighty, to duely reward you for these acts of worship. Your menses start once you see blood because the situation remains as such unless there is certainty or predominant conjecture, as per the Fiqh maxim: "Certainty is not removed by doubt". And Allah Knows Best.

Is it incumbent on a father to cover the marriage costs of his son if the latter couldn`t afford them?

The son should seek the help of his relatives in order to convince his father to do the aforesaid, and the father should make sure that his son doesn`t commit fornication through helping him to get married, and Allah will reward him for doing so.

Is the father a Mahram (Non-marriageable) to his son`s mother-in-law?

The father is a non-Mahram (Marriageable) to his son`s mother-in-law, so it is impermissible for them to look at each other, or to have a seclusion (Khalwah).

Is it permissible for one to shake hands with his uncle`s daughter?

No, it isn`t because he is a non-Mahram (Marriageable) to her.