What is the ruling on water present on the floor of a toilet/bathroom?
The default ruling is the purity of this water present on the bathroom floor. If one is certain or strongly suspects its impurity, then one washes whatever part of the body or clothing this impure water has touched. If one doubts its impurity, the default is purity, and we do not rule it impure based on mere doubt. And Allah the Almighty 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.
What is the ruling on using a miswak (tooth-stick) during the day in Ramadan?
It is permissible to use a miswak before noon while fasting. However, according to the Shafi'i school, it is disliked (makruh) after noon in order to preserve the natural effect of fasting in the mouth, as the Prophetﷺ said in authentic hadith:
"The breath of a fasting person is more pleasant to Allah than the fragrance of musk."
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.