Is washing the private part after urinating (Istinjaa`) a condition, and is it done with water and soap, or with water only?
Istinjaa` is obligatory for removing impurity, and it can be done with toilet paper, or a stone, or water. It is preferable to do Istinjaa` first with paper, or stone, or the like, then to wash the private part with water until making sure that the impurity has been removed. Using soap is not a condition, but there is no harm in doing so provided that it is washed off with water. It is also permissible to use either water, or paper if impurity is removed by any.
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 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.
What is the ruling on reciting verses from the Qur'an over water, drinking it, and using it to break magic spells, heal illnesses, or burn jinn?
There is no harm on reciting verses of the Holy Qur'an over water and use it for cure. And Allah Knows Best.