What is the ruling on making up missed fasts from many years?
A Muslim must make up for any missed fasts, as they are a debt owed to Allah. The Prophet ﷺ said:
"The debt owed to Allah is more deserving of being fulfilled." [Narrated by Muslim]
Whoever has missed fasts must make them up as long as they are alive and capable of fasting.
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.
What is the ruling on istinja' after urination, and is it done with water and soap or with water only?
Istinja' from urine and stool is obligatory. It is permissible to perform istinja' with water alone, or with toilet paper alone. The best way is with toilet paper then water. If one wishes to suffice with one of them, then water is better. And Allah the Almighty knows best.
Should the Zakah (obligatory charity) giver tell the poor recipient that this is the Zakah of his money?
No, he shouldn`t. But, the Zakah giver should make an intention in his heart that it is the Zakah of his money when paying it to the poor. And Allah Knows Best.