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 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.
I`m a pious Muslim woman, but my husband isn`t, what should I do?
You should exercise patience, make supplication that Allah guides him to the straight path, and keep advising him kindly.
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.