What is the ruling on entering the toilet with something containing the remembrance of Allah?
It is disliked to bring into the toilet anything containing a reminder of Allah, such as the Quran or a sacred name (like the name of Allah, Muhammad, etc.). If one does that, etiquette dictates that he conceal it so it is not visible while entering the toilet, either by cupping his hands over it, putting it in his pocket, or inside his shirt if it is a necklace or ring. And Allah the Almighty knows best.
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.
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.