Is Zakah (obligatory charity) due on the Zakah money received by a poor person, and reached a Nissab (minimum amount liable for Zakah), and a whole lunar year had lapsed over having it in his possession?
Yes, the poor who possessed a Nissab for a whole lunar year is obliged to pay the Zakah due on that money even if it was given to him as a Zakah money in the first place. And Allah Knows Best.
What is the ruling on swearing on the Holy Quran and breaking that oath?
It is impermissible to swear on the Holy Quran in vain, and it is also impermissible to subject it to such an act since breaking the oath after swearing on the Quran entails an expiation.
Is supplicating in Qunoot, at times of affliction, during obligatory and voluntary prayer a Sunnah, and should it be done before Rukoo` (bowing), or after it?
At times of affliction, it is a Sunnah that Muslims supplicate in Qunoot after the final Rukoo` of each obligatory, or voluntary prayer as individuals, or in congregation.
What is the ruling on performing istinja' before every ablution?
Istinja' is not from the conditions for the validity of ablution. It is only obligatory for prayer when there is impurity from urine or stool on the private part, or if there is fear of the impurity spreading to the body or clothing. And Allah the Almighty knows best.