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.
Is it a condition that a woman should untie her locks while making Ghusl (ritual bath)?
Ghusl from Janabah (ritual impurity), or menstruation obligates that water reaches the roots of the hair in order for the Ghusl to be valid, but if it doesn`t, then hair locks must be untied for water to reach them, and for Ghusl to become valid.
What is the ruling on someone who prays Fajr late, after sunrise, knowing that they wake up on time but return to sleep and do not perform it within its time?
It is obligatory to perform the prayer within its prescribed time. If someone wakes up and knows how to act, they must perform it before the time ends. If they delay it, they are sinful and must make it up. And Allah Knows Best.
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.