How should I deal with the whispers of the devil with regard to ablution and purity?
Whispers in ablution are from the devil, and so you should take refuge in Allah from the devil`s evil suggestions that aim to distort the religion. Thus, once an organ is completely pure, don`t question its purity since having whispers doesn`t mean that the purity is invalid as it has already been established.
What is the ruling on someone who perform their prayer after finishing it because they believe they missed a Rak'a, a prostration, or that they did not perform it correctly (thinking their prayer was invalid)?
If he was sure that his prayer is void then reperforming it is an obligation along with figuring out the reason of invalidity so long as this wasn't out of uncertainty. And Allah Knows Best.
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 should one who forgot to offer the second Sajda during congregational prayer, and remembered it before the end of the prayer do?
All perfect praise be to Allah, The Lord of The Worlds. Whoever forgets a pillar of prayer while in congregation must follow the lead of the Imam, and after the latter offers Tasleem, he should offer one Rakah, then perform Sujood As-Sahw (prostration of forgetfulness). And Allah Knows Best.