How do I deal with whispers (waswasa) in ablution and purification?
Whispers in ablution are from Satan, and the Muslim should not pay attention to them. He is not required to re-perform ablution or repeat washing a limb because of waswasa. He should always base his purification on its being valid. It is recommended for him to frequently say "La ilaha illa Allah" (There is no god but Allah), because Satan recoils when Allah is mentioned. And Allah the Almighty knows best.
Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
What is the ruling on performing istinja' with perfumed tissues or a tissue moistened with water?
Performing istinja' with perfumed or moistened tissues is not sufficient if they are not dry, due to the moisture on them reaching the impurity, which increases its spread rather than reducing it. Then, to remove the impurity, one must use pure water. 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.