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.
Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
Is it obligatory to have the intention for each day of fasting, or is one intention sufficient for the whole month?
The intention is obligatory for each day of Ramadan because each day is an independent act of worship separate from the others.
The intention must be made at night before the break of dawn, as the Prophetﷺ said: "Whoever does not intend fasting at night, there is no fast for him." [An-Nasa’i]
And he also said: "Whoever does not firmly resolve to fast before dawn, there is no fast for him." [At-Tirmidhi, Abu Dawood, and An-Nasa’i]
Whoever wakes up and eats Suhoor while mindful of fasting has made the intention. Likewise, one who firmly intends at any moment during the night to fast the next day has also fulfilled the intention.
What should a person who doubted having missed a pillar of prayer do?
All praise be to Allah, The Lord of The Worlds. The prayer of one who doubts having missed one of its pillars is valid, and nothing is due on him/her since having a doubt after offering the act of worship doesn`t undermine its validity. And Allah Knows Best.