Is it permissible for the children of a deceased father to settle his debt from the Zakah (obligatory charity) money due on them?
It is impermissible to use the Zakah of one`s money for settling the debts of the deceased. However, children should settle the debts of their deceased parents out of filial piety. And Allah Knows Best.
What is the ruling on istinja' after urination, and is it done with water and soap or with water only?
Istinja' from urine and stool is obligatory. It is permissible to perform istinja' with water alone, or with toilet paper alone. The best way is with toilet paper then water. If one wishes to suffice with one of them, then water is better. And Allah the Almighty knows best.
How many prostrations of Quranic recital are there, and is it permissible not to offer them while reciting?
There is one prostration for the Quranic recital, and it is a Sunnah for which one is rewarded upon offering it. However, one who doesn`t isn`t punished. Therefore, those who fail to offer it aren`t considered sinful, rather they deprive themselves from the reward.
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.