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.
What is the ruling on preparing food for someone who is not fasting in Ramadan?
It is forbidden to prepare food for someone who is breaking their fast without a valid excuse in Ramadan.
Doing so would be assisting in sin, and assisting in sin is itself a sin.
Allah says {what means}: "but help ye not one another in sin and rancour" [Al-Mai`dah/2]
What is the ruling on using a miswak (tooth-stick) during the day in Ramadan?
It is permissible to use a miswak before noon while fasting. However, according to the Shafi'i school, it is disliked (makruh) after noon in order to preserve the natural effect of fasting in the mouth, as the Prophetﷺ said in authentic hadith:
"The breath of a fasting person is more pleasant to Allah than the fragrance of musk."
Who should pay the Zakah (obligatory charity) from the orphan`s money?
His/her guardian, and if the latter fails to do so, then the orphan himself/herself is obliged to pay the Zakah once he/she reaches puberty, and is capable of handling his/her own affairs. And Allah Knows Best.