What is the ruling on istibra' and how is it performed?
Istibra' (cleansing from urine) is recommended. It is for a person to ensure that nothing remains of urine in its passage before performing istinja'. Its method is: to clear the throat (or cough slightly), shake the penis (meaning to pass fingers along it to expel any remaining urine if needed), and walk a few steps to the extent that one thinks nothing of urine remains if walking is needed. Each person knows his own nature best. The preferred opinion is that this differs among people. The objective is for one to think that nothing remains in the urinary passage that he fears will exit later. And Allah the Almighty knows best.
What is the ruling on performing istinja' after passing wind from the anus?
Ablution is invalidated by passing wind from the anus, even without a smell. Only ablution becomes obligatory from it. Istinja' is not obligatory nor recommended. And Allah the Almighty knows best.
What is the ruling on performing ablution (wudu') and ritual bathing (ghusl) with Zamzam water?
It is permissible to perform ablution and ritual bathing with Zamzam water. However, scholars disliked using it for cleaning after relieving oneself (istinja'). And Allah the Almighty knows best.
Is it permissible for a praying person to make supplication in each Sajdah (a prostration) of obligatory prayer?
It is permissible for a praying person, whether praying individually, or in congregation, to make supplication during Sujood (prostration) in obligatory, or voluntary prayers. However, it is disliked for the Imam to do so since he is required to spare the prayer performers any sort of hardship, unless he is leading a certain group who don`t mind him extending the prayer.