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.
I took a car from the Orphans' Fund Development Institution; is there usury (Riba) involved in this transaction?
If the Sharia's conditions were met, then there is no harm in this. And Allah The Exalted Knows Best.
Is it permissible for a mother to stop her daughter from marrying a respectable, God-fearing young man because he isn't college/university graduate?
It is impermissible to deny a woman her right in getting married except for a lawful reason, and problems can be solved through dialogue. However, she can file a suit in order for the judge to have a say in that regard.
I underwent a procedure for a molar pregnancy (hydatidiform mole), and after that, the bleeding continued for more than two months, during which I did not pray. Do I need to make up the missed prayers?
If you have previously experienced postpartum bleeding, the duration of the current bleeding is treated the same as your previous postpartum period. Any bleeding that exceeds this duration must be considered irregular bleeding (istihada), and you must make up the missed prayers. If this is the first time, then any bleeding beyond sixty days is considered irregular bleeding. You must perform ghusl, pray, and make up the prayers for the days beyond the sixty-day limit. And Allah Knows Best.