Is it permissible for someone to make a supplication to Allah to marry an already married, or an engaged woman?
No, it isn`t, and the person who does so is sinful before Allah, The Almighty.
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 Zakah (obligatory charity) due on articles of merchandise even if they were stacked in the merchant`s stores for years?
Yes, Zakah is due on goods even if they were stacked in merchant`s stores for years, in this manner Islam struggle against monopoly.
A woman has asked her husband for Khulu`, her gold, deferred portion of the dowry and furniture. Is she entitled to that, knowing that her husband doesn`t want to divorce her?
All perfect praise be to Allah the Lord of the Worlds. May His peace and blessings be upon Prophet Mohammad and upon all his family and companions.
Khulu`* can`t takes place save before a judge of Sharia and he has the authority to make the suitable decision in this matter. And Allah The Almighty Knows Best.
* Khulu' is when parties agree to separate by way of consent, usually upon terms such as the wife agreeing to repay her Mahr (dowry) to the husband upon him agreeing to grant Talaq. The iddah period (waiting time after a divorce) of a woman who seeks a khula, is one menstrual cycle or one month if she is post-menopause i.e. ceased menstruating. This is to ensure she is not pregnant. This differs from when a man gives a talaq; the iddah period is three cycles or three months.