Is Zakah(obligatory charity) due on the Zakah money received by a poor person, and reached a Nissab( minimum amount liable for Zakah), and a whole lunar year had lapsed over having it in his possession?

Yes, the poor who possessed a Nissab for a whole lunar year is obliged to pay the Zakah due on that money even if it was given to him as a Zakah money in the first place.

What is the ruling on performing voluntary prayers during official working hours?

All perfect praise be to Allah, The Lord of The Worlds, and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his family and companions

There is no harm if  there was break time during official working hours, but if not then it is impermissible. And Allah Knows Best.

Is it permissible for a person who broke fasting in Ramadhaan because of being sick to pay a ransom?

If there is hope for him/her to be cured, then he would be required to make up for the missed fasting days when he/she recovers, and no ransom is due on him/her. If his/her disease is incurable, then he/she would be required to pay a ransom for each missed fasting day, which is (600) grams of wheat, or rice.

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.