Is prayer nullified by having thoughts while performing it?
Prayer isn`t nullified by having thoughts while performing it, provided that the praying person offers all of its pillars and meets all of its conditions. However, the reward decreases significantly in the absence of reverence since a praying person is rewarded according to the attentiveness of his/her heart during prayer.
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 a praying person who doubts having offered one, or two prostrations in the third Rakah (unit of prayer) do?
Whoever has doubts about their prayer should consider what is less i.e. the above person should offer another Sajda (prostration) and complete his/her prayer, then offer Sujood As-Sahw (prostration of forgetfulness). And Allah Knows Best.
Islamic creed is a comprehensive creed, and if there is any defect, the creed of the individual or group is not correct. Is the creed of the Sufis correct or not?
Sufism is the practice of applying knowledge; this is how Al-Imam Al-Sha'rani defined it. If some among them have deviations in creed, it is not permissible to generalize this to all Sufis, as there are those among them who are acknowledged by all scholars for their knowledge and virtue. And Allah The Almighty Knows Best.