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)?
If he was sure that his prayer is void then reperforming it is an obligation along with figuring out the reason of invalidity so long as this wasn't out of uncertainty. And Allah Knows Best.
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.
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 for a man to marry up to four wives (polygamy in Islam) for pleasure although he can`t afford that?
It is desirable for the man to have one wife if there was no need for him to have more, if he can't afford marriage forthcoming expenses.