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.
What should a woman who delayed making up for missed fast, due to menstruation, till the start of the next Ramadan?
Whosoever broke fasting in Ramadan, and was able to make up for it, but didn`t until the next Ramadan started, is obliged to make up for the missed days, and to pay the ransom as well. However, if he/she wasn`t able to before next Ramadhaan due to an excuse, then he/she should only make up for the missed days. 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.
Is it permissible for one to shake hands with his uncle`s daughter?
No, it isn`t because he is a non-Mahram (Marriageable) to her.